RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.MV5w0N/RM_1522849.MonJan131456062025 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: 1736808966 Database = /data/tmp/rModeler.MV5w0N/GCA_007570765.1_GSC_moose_1.0 - Sequences = 47840 - Bases = 2742408694 - N50 = 4131254 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 34107365-36543544 | [ 1 ] 31671186-34107364 | [ 1 ] 29235007-31671185 | [ ] 26798828-29235006 | [ ] 24362649-26798827 | [ 1 ] 21926470-24362648 | [ ] 19490291-21926469 | [ 1 ] 17054113-19490291 | [ 2 ] 14617934-17054112 | [ 3 ] 12181755-14617933 | [ 3 ] 9745576-12181754 | [ 21 ] 7309397-9745575 | [ 35 ] 4873218-7309396 | [ 74 ] 2437039-4873217 | [ 170 ] 861-2437039 |************************************************** [ 47528 ] Storage Throughput = excellent ( 1690.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43159389 bp ( 40025400 non ambiguous ) - Num Contigs Represented = 1165 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:29 (hh:mm:ss) Elapsed Time Round Time: 00:12:14 (hh:mm:ss) Elapsed Time : 255 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14176 repeats masked totaling 2971792 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10954424 bp Num Contigs Represented = 362 Non ambiguous bp: Initial: 10024040 bp After Masking: 7023150 bp Masked: 29.94 % -- Input Database Coverage: 10954424 bp out of 2742408694 bp ( 0.40 % ) Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 88410 Comparison Time: 00:03:32 (hh:mm:ss) Elapsed Time, 13564 HSPs Collected Number of families returned by RECON: 766 Round Time: 00:04:05 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46987 repeats masked totaling 9802451 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32204885 bp Num Contigs Represented = 927 Non ambiguous bp: Initial: 30001280 bp After Masking: 20115295 bp Masked: 32.95 % -- Input Database Coverage: 43159309 bp out of 2742408694 bp ( 1.57 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 768180 Comparison Time: 00:17:06 (hh:mm:ss) Elapsed Time, 25191 HSPs Collected Number of families returned by RECON: 2343 Round Time: 00:18:21 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149343 repeats masked totaling 31531785 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 97566743 bp Num Contigs Represented = 2273 Non ambiguous bp: Initial: 90036314 bp After Masking: 58283279 bp Masked: 35.27 % -- Input Database Coverage: 140726052 bp out of 2742408694 bp ( 5.13 % ) Sampling Time: 00:02:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 7233306 Comparison Time: 01:47:39 (hh:mm:ss) Elapsed Time, 73700 HSPs Collected Number of families returned by RECON: 7944 Round Time: 01:51:39 (hh:mm:ss) Elapsed Time : 149 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 473135 repeats masked totaling 101533088 bp(s). - TE Masking time 00:03:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 291429167 bp Num Contigs Represented = 6023 Non ambiguous bp: Initial: 270004426 bp After Masking: 167838745 bp Masked: 37.84 % -- Input Database Coverage: 432155219 bp out of 2742408694 bp ( 15.76 % ) Sampling Time: 00:08:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 66730128 Comparison Time: 11:03:01 (hh:mm:ss) Elapsed Time, 223518 HSPs Collected Number of families returned by RECON: 34545 Round Time: 11:19:55 (hh:mm:ss) Elapsed Time : 356 families discovered. RepeatScout/RECON discovery complete: 843 families found Classification Time: 00:15:39 (hh:mm:ss) Elapsed Time Program Time: 14:01:53 (hh:mm:ss) Elapsed Time