RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.7V4CZH/RM_26320.TueJul91751032024 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: 1720572662 Database = /dev/shm/rModeler.7V4CZH/GCF_001660625.3_Coco_2.0 - Sequences = 137 - Bases = 842942949 - N50 = 29879606 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 37544604-40225253 |* [ 3 ] 34863956-37544604 |* [ 3 ] 32183308-34863956 |* [ 3 ] 29502660-32183308 |* [ 3 ] 26822012-29502660 |** [ 5 ] 24141363-26822011 |* [ 3 ] 21460715-24141363 | [ 2 ] 18780067-21460715 |** [ 6 ] 16099419-18780067 | [ 1 ] 13418771-16099419 | [ ] 10738122-13418770 | [ ] 8057474-10738122 | [ ] 5376826-8057474 | [ 1 ] 2696178-5376826 | [ 2 ] 15530-2696178 |************************************************** [ 105 ] Storage Throughput = excellent ( 1171.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40117407 bp ( 40031667 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:20 (hh:mm:ss) Elapsed Time Round Time: 00:34:10 (hh:mm:ss) Elapsed Time : 685 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13950 repeats masked totaling 2499360 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039093 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10003550 bp After Masking: 6644442 bp Masked: 33.58 % -- Input Database Coverage: 10039093 bp out of 842942949 bp ( 1.19 % ) Sampling Time: 00:02:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:46 (hh:mm:ss) Elapsed Time, 12249 HSPs Collected Number of families returned by RECON: 1676 Round Time: 00:08:25 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44274 repeats masked totaling 7944348 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30078304 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30028107 bp After Masking: 19939877 bp Masked: 33.60 % -- Input Database Coverage: 40117397 bp out of 842942949 bp ( 4.76 % ) Sampling Time: 00:07:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:32:09 (hh:mm:ss) Elapsed Time, 62264 HSPs Collected Number of families returned by RECON: 5387 Round Time: 00:42:44 (hh:mm:ss) Elapsed Time : 125 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 144987 repeats masked totaling 25513832 bp(s). - TE Masking time 00:02:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90714411 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 90031280 bp After Masking: 58128913 bp Masked: 35.43 % -- Input Database Coverage: 130831808 bp out of 842942949 bp ( 15.52 % ) Sampling Time: 00:20:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 03:51:04 (hh:mm:ss) Elapsed Time, 338255 HSPs Collected Number of families returned by RECON: 17260 Round Time: 04:29:30 (hh:mm:ss) Elapsed Time : 543 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:55:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 504144 repeats masked totaling 96414625 bp(s). - TE Masking time 00:16:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271558776 bp Num Contigs Represented = 96 Non ambiguous bp: Initial: 270002751 bp After Masking: 154040318 bp Masked: 42.95 % -- Input Database Coverage: 402390584 bp out of 842942949 bp ( 47.74 % ) Sampling Time: 01:16:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23205078 Comparison Time: 28:25:22 (hh:mm:ss) Elapsed Time, 808459 HSPs Collected Number of families returned by RECON: 51462 Round Time: 31:17:35 (hh:mm:ss) Elapsed Time : 1101 families discovered. RepeatScout/RECON discovery complete: 2475 families found Classification Time: 01:57:15 (hh:mm:ss) Elapsed Time Program Time: 39:09:39 (hh:mm:ss) Elapsed Time