RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GENU8E/RM_2487.MonJan20838462023 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: 1672677525 Database = /dev/shm/rModeler.GENU8E/GCF_905171775.1_aRanTem1.1 - Sequences = 554 - Bases = 4111422596 - N50 = 495417988 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 644610770-690654357 | [ 1 ] 598567184-644610770 | [ ] 552523598-598567184 | [ ] 506480011-552523597 | [ 1 ] 460436425-506480011 | [ 2 ] 414392839-460436425 | [ 1 ] 368349253-414392839 | [ ] 322305666-368349252 | [ ] 276262080-322305666 | [ ] 230218494-276262080 | [ ] 184174908-230218494 | [ 4 ] 138131321-184174907 | [ 3 ] 92087735-138131321 | [ 1 ] 46044149-92087735 | [ ] 563-46044149 |************************************************** [ 541 ] Storage Throughput = excellent ( 1167.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40252240 bp ( 40034268 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:08:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:32 (hh:mm:ss) Elapsed Time Round Time: 00:34:18 (hh:mm:ss) Elapsed Time : 1222 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21815 repeats masked totaling 5410764 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040108 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 10039795 bp After Masking: 4012835 bp Masked: 60.03 % -- Input Database Coverage: 10040108 bp out of 4111422596 bp ( 0.24 % ) Sampling Time: 00:03:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:04 (hh:mm:ss) Elapsed Time, 9340 HSPs Collected Number of families returned by RECON: 1470 Round Time: 00:08:47 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:06:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66648 repeats masked totaling 16160243 bp(s). - TE Masking time 00:01:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30252052 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30034393 bp After Masking: 11829615 bp Masked: 60.61 % -- Input Database Coverage: 40292160 bp out of 4111422596 bp ( 0.98 % ) Sampling Time: 00:11:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:20:39 (hh:mm:ss) Elapsed Time, 56074 HSPs Collected Number of families returned by RECON: 4994 Round Time: 00:33:55 (hh:mm:ss) Elapsed Time : 114 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:19:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 205840 repeats masked totaling 49204870 bp(s). - TE Masking time 00:02:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90498823 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90004405 bp After Masking: 34194638 bp Masked: 62.01 % -- Input Database Coverage: 130790983 bp out of 4111422596 bp ( 3.18 % ) Sampling Time: 00:33:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 01:48:18 (hh:mm:ss) Elapsed Time, 308172 HSPs Collected Number of families returned by RECON: 13474 Round Time: 02:32:22 (hh:mm:ss) Elapsed Time : 638 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:58:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 696713 repeats masked totaling 164977161 bp(s). - TE Masking time 00:14:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271714386 bp Num Contigs Represented = 108 Non ambiguous bp: Initial: 270013711 bp After Masking: 85936289 bp Masked: 68.17 % -- Input Database Coverage: 402505369 bp out of 4111422596 bp ( 9.79 % ) Sampling Time: 01:46:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23232336 Comparison Time: 13:03:15 (hh:mm:ss) Elapsed Time, 917279 HSPs Collected Number of families returned by RECON: 33460 Round Time: 16:20:43 (hh:mm:ss) Elapsed Time : 1643 families discovered. RepeatScout/RECON discovery complete: 3635 families found Classification Time: 02:03:46 (hh:mm:ss) Elapsed Time Program Time: 22:13:51 (hh:mm:ss) Elapsed Time