RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.aNDgXV/RM_2103458.FriDec10109542023 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: 1701421793 Database = /dev/shm/rModeler.aNDgXV/GCF_028018845.1_bMelGeo1.pri - Sequences = 40 - Bases = 1162015399 Storage Throughput = excellent ( 1348.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40075439 bp ( 40039330 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:57 (hh:mm:ss) Elapsed Time Round Time: 00:21:55 (hh:mm:ss) Elapsed Time : 176 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3114 repeats masked totaling 874060 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036416 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10008106 bp After Masking: 8338498 bp Masked: 16.68 % -- Input Database Coverage: 10036416 bp out of 1162015399 bp ( 0.86 % ) Sampling Time: 00:01:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:57 (hh:mm:ss) Elapsed Time, 3834 HSPs Collected Number of families returned by RECON: 309 Round Time: 00:08:18 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10045 repeats masked totaling 2812486 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039000 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30031201 bp After Masking: 25283442 bp Masked: 15.81 % -- Input Database Coverage: 40075416 bp out of 1162015399 bp ( 3.45 % ) Sampling Time: 00:03:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:33:35 (hh:mm:ss) Elapsed Time, 7091 HSPs Collected Number of families returned by RECON: 1836 Round Time: 00:37:20 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28010 repeats masked totaling 8512762 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90206145 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 90030616 bp After Masking: 75518559 bp Masked: 16.12 % -- Input Database Coverage: 130281561 bp out of 1162015399 bp ( 11.21 % ) Sampling Time: 00:10:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 03:35:43 (hh:mm:ss) Elapsed Time, 73696 HSPs Collected Number of families returned by RECON: 10685 Round Time: 03:53:20 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 99276 repeats masked totaling 30551807 bp(s). - TE Masking time 00:04:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270342150 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 270028067 bp After Masking: 222853819 bp Masked: 17.47 % -- Input Database Coverage: 400623711 bp out of 1162015399 bp ( 34.48 % ) Sampling Time: 00:32:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22865703 Comparison Time: 27:05:36 (hh:mm:ss) Elapsed Time, 312409 HSPs Collected Number of families returned by RECON: 71762 Round Time: 29:20:38 (hh:mm:ss) Elapsed Time : 294 families discovered. RepeatScout/RECON discovery complete: 600 families found Classification Time: 00:59:16 (hh:mm:ss) Elapsed Time Program Time: 35:20:47 (hh:mm:ss) Elapsed Time