RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MoaQsu/RM_1100372.WedMar201214212024 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: 1710962061 Database = /dev/shm/rModeler.MoaQsu/GCA_036365495.1_sHetFra1.hap2 - Sequences = 1496 - Bases = 5196885747 - N50 = 98251988 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 268839884-288041747 | [ 1 ] 249638022-268839884 | [ ] 230436159-249638021 | [ 1 ] 211234297-230436159 | [ 2 ] 192032435-211234297 | [ 1 ] 172830572-192032434 | [ ] 153628710-172830572 | [ 1 ] 134426847-153628709 | [ 1 ] 115224985-134426847 | [ 6 ] 96023123-115224985 | [ 4 ] 76821260-96023122 | [ 6 ] 57619398-76821260 | [ 9 ] 38417535-57619397 | [ 8 ] 19215673-38417535 | [ 9 ] 13811-19215673 |************************************************** [ 1447 ] Storage Throughput = excellent ( 1302.70 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40221731 bp ( 40018555 non ambiguous ) - Num Contigs Represented = 186 - Sequence extraction : 00:02:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:00 (hh:mm:ss) Elapsed Time Round Time: 00:29:56 (hh:mm:ss) Elapsed Time : 586 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15965 repeats masked totaling 4924232 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10043253 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 10027949 bp After Masking: 2619244 bp Masked: 73.88 % -- Input Database Coverage: 10043253 bp out of 5196885747 bp ( 0.19 % ) Sampling Time: 00:10:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:49 (hh:mm:ss) Elapsed Time, 3714 HSPs Collected Number of families returned by RECON: 631 Round Time: 00:14:05 (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 : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49570 repeats masked totaling 15757396 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30218398 bp Num Contigs Represented = 154 Non ambiguous bp: Initial: 30030526 bp After Masking: 7741687 bp Masked: 74.22 % -- Input Database Coverage: 40261651 bp out of 5196885747 bp ( 0.77 % ) Sampling Time: 00:27:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:17:15 (hh:mm:ss) Elapsed Time, 24674 HSPs Collected Number of families returned by RECON: 1975 Round Time: 00:45:58 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:19:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153568 repeats masked totaling 48290282 bp(s). - TE Masking time 00:02:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90399831 bp Num Contigs Represented = 273 Non ambiguous bp: Initial: 90003961 bp After Masking: 22210619 bp Masked: 75.32 % -- Input Database Coverage: 130661482 bp out of 5196885747 bp ( 2.51 % ) Sampling Time: 01:26:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 01:22:09 (hh:mm:ss) Elapsed Time, 128035 HSPs Collected Number of families returned by RECON: 5448 Round Time: 02:51:52 (hh:mm:ss) Elapsed Time : 239 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:36:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 500381 repeats masked totaling 155765425 bp(s). - TE Masking time 00:07:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271343812 bp Num Contigs Represented = 526 Non ambiguous bp: Initial: 270011300 bp After Masking: 59112803 bp Masked: 78.11 % -- Input Database Coverage: 402005294 bp out of 5196885747 bp ( 7.74 % ) Sampling Time: 03:59:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23252790 Comparison Time: 08:40:30 (hh:mm:ss) Elapsed Time, 352186 HSPs Collected Number of families returned by RECON: 15896 Round Time: 12:53:30 (hh:mm:ss) Elapsed Time : 588 families discovered. RepeatScout/RECON discovery complete: 1483 families found Classification Time: 00:57:01 (hh:mm:ss) Elapsed Time Program Time: 18:12:22 (hh:mm:ss) Elapsed Time