RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MoR31J/RM_2464563.ThuNov300124502023 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: 1701336290 Database = /dev/shm/rModeler.MoR31J/GCF_029633865.1_fLamInc1.hap2 - Sequences = 544 - Bases = 1482357630 - N50 = 69029564 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 144672129-155004971 | [ 2 ] 134339287-144672128 | [ ] 124006445-134339286 | [ ] 113673603-124006444 | [ 1 ] 103340761-113673602 | [ ] 93007919-103340760 | [ ] 82675077-93007918 | [ ] 72342236-82675077 | [ 1 ] 62009394-72342235 | [ 5 ] 51676552-62009393 | [ 5 ] 41343710-51676551 | [ 4 ] 31010868-41343709 | [ 2 ] 20678026-31010867 | [ 1 ] 10345184-20678025 | [ ] 12343-10345184 |************************************************* [ 523 ] Storage Throughput = excellent ( 1174.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036162 bp ( 40020283 non ambiguous ) - Num Contigs Represented = 64 - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:47 (hh:mm:ss) Elapsed Time Round Time: 00:30:27 (hh:mm:ss) Elapsed Time : 606 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10039 repeats masked totaling 3196870 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004923 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 9999923 bp After Masking: 5472522 bp Masked: 45.27 % -- Input Database Coverage: 10004923 bp out of 1482357630 bp ( 0.67 % ) Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:12:05 (hh:mm:ss) Elapsed Time, 238659 HSPs Collected Number of families returned by RECON: 1310 Round Time: 00:16:49 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31132 repeats masked totaling 9723570 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031159 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30020280 bp After Masking: 16307346 bp Masked: 45.68 % -- Input Database Coverage: 40036082 bp out of 1482357630 bp ( 2.70 % ) Sampling Time: 00:10:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:39:17 (hh:mm:ss) Elapsed Time, 1288125 HSPs Collected Number of families returned by RECON: 4376 Round Time: 00:52:00 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 97334 repeats masked totaling 30299779 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90059640 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 90023868 bp After Masking: 46701385 bp Masked: 48.12 % -- Input Database Coverage: 130095722 bp out of 1482357630 bp ( 8.78 % ) Sampling Time: 00:36:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 04:22:49 (hh:mm:ss) Elapsed Time, 16649377 HSPs Collected Number of families returned by RECON: 12055 Round Time: 05:14:05 (hh:mm:ss) Elapsed Time : 618 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:27:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 370212 repeats masked totaling 110819007 bp(s). - TE Masking time 00:11:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270147954 bp Num Contigs Represented = 221 Non ambiguous bp: Initial: 270034760 bp After Masking: 121750482 bp Masked: 54.91 % -- Input Database Coverage: 400243676 bp out of 1482357630 bp ( 27.00 % ) Sampling Time: 01:50:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23116600 Comparison Time: 27:41:46 (hh:mm:ss) Elapsed Time, 115974460 HSPs Collected Number of families returned by RECON: 33009 Round Time: 31:47:41 (hh:mm:ss) Elapsed Time : 1498 families discovered. RepeatScout/RECON discovery complete: 2826 families found Classification Time: 02:45:42 (hh:mm:ss) Elapsed Time Program Time: 41:26:44 (hh:mm:ss) Elapsed Time