RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.POOqkb/RM_11644.TueJan101517222023 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: 1673392641 Database = /dev/shm/rModeler.POOqkb/GCF_010909765.2_sAmbRad1.1.pri - Sequences = 957 - Bases = 2558784953 - N50 = 62869304 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 180290507-193168304 | [ 1 ] 167412711-180290507 | [ ] 154534915-167412711 | [ ] 141657119-154534915 | [ 1 ] 128779323-141657119 | [ 1 ] 115901527-128779323 | [ 1 ] 103023731-115901527 | [ 2 ] 90145935-103023731 | [ 1 ] 77268139-90145935 | [ 1 ] 64390343-77268139 | [ 3 ] 51512547-64390343 | [ 5 ] 38634751-51512547 | [ 8 ] 25756955-38634751 | [ 10 ] 12879159-25756955 | [ 11 ] 1363-12879159 |************************************************** [ 912 ] Storage Throughput = good ( 944.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43126888 bp ( 40025783 non ambiguous ) - Num Contigs Represented = 92 - Sequence extraction : 00:01:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:09 (hh:mm:ss) Elapsed Time Round Time: 00:29:48 (hh:mm:ss) Elapsed Time : 724 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31226 repeats masked totaling 5954502 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10741699 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 10037114 bp After Masking: 3826000 bp Masked: 61.88 % -- Input Database Coverage: 10741699 bp out of 2558784953 bp ( 0.42 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36315 Comparison Time: 00:06:19 (hh:mm:ss) Elapsed Time, 3490 HSPs Collected Number of families returned by RECON: 558 Round Time: 00:08:26 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 93005 repeats masked totaling 17960881 bp(s). - TE Masking time 00:01:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32425033 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 30028513 bp After Masking: 11307709 bp Masked: 62.34 % -- Input Database Coverage: 43166732 bp out of 2558784953 bp ( 1.69 % ) Sampling Time: 00:05:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 332520 Comparison Time: 00:25:50 (hh:mm:ss) Elapsed Time, 20705 HSPs Collected Number of families returned by RECON: 1776 Round Time: 00:32:16 (hh:mm:ss) Elapsed Time : 43 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 283036 repeats masked totaling 54730926 bp(s). - TE Masking time 00:04:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 97473960 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 90028467 bp After Masking: 32824783 bp Masked: 63.54 % -- Input Database Coverage: 140640692 bp out of 2558784953 bp ( 5.50 % ) Sampling Time: 00:18:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2995128 Comparison Time: 02:21:57 (hh:mm:ss) Elapsed Time, 120323 HSPs Collected Number of families returned by RECON: 5214 Round Time: 02:44:03 (hh:mm:ss) Elapsed Time : 279 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 899857 repeats masked totaling 172408038 bp(s). - TE Masking time 00:17:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 293445612 bp Num Contigs Represented = 296 Non ambiguous bp: Initial: 270026825 bp After Masking: 90160962 bp Masked: 66.61 % -- Input Database Coverage: 434086304 bp out of 2558784953 bp ( 16.96 % ) Sampling Time: 00:52:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 27331921 Comparison Time: 15:41:33 (hh:mm:ss) Elapsed Time, 313159 HSPs Collected Number of families returned by RECON: 15455 Round Time: 16:50:57 (hh:mm:ss) Elapsed Time : 558 families discovered. RepeatScout/RECON discovery complete: 1609 families found Classification Time: 01:12:57 (hh:mm:ss) Elapsed Time Program Time: 21:58:27 (hh:mm:ss) Elapsed Time