RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ii68oV/RM_1842014.SunJul200314242025 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: 1753006464 Database = /dev/shm/rModeler.ii68oV/GCA_963921485.1_norwegian_landrace - Sequences = 54 - Bases = 2633804377 Storage Throughput = excellent ( 1671.28 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029508 bp ( 40029508 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:51 (hh:mm:ss) Elapsed Time Round Time: 00:11:32 (hh:mm:ss) Elapsed Time : 178 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12280 repeats masked totaling 2711803 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000320 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000320 bp After Masking: 6866475 bp Masked: 31.34 % -- Input Database Coverage: 10000320 bp out of 2633804377 bp ( 0.38 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 20813 HSPs Collected Number of families returned by RECON: 722 Round Time: 00:04:04 (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 : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42407 repeats masked totaling 9433083 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029108 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30029108 bp After Masking: 19463978 bp Masked: 35.18 % -- Input Database Coverage: 40029428 bp out of 2633804377 bp ( 1.52 % ) Sampling Time: 00:01:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:12:54 (hh:mm:ss) Elapsed Time, 48218 HSPs Collected Number of families returned by RECON: 2028 Round Time: 00:15:06 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 133698 repeats masked totaling 29506931 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003417 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 90003417 bp After Masking: 56911593 bp Masked: 36.77 % -- Input Database Coverage: 130032845 bp out of 2633804377 bp ( 4.94 % ) Sampling Time: 00:06:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:08:24 (hh:mm:ss) Elapsed Time, 91563 HSPs Collected Number of families returned by RECON: 8085 Round Time: 01:16:26 (hh:mm:ss) Elapsed Time : 168 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 434659 repeats masked totaling 96160562 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270025264 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 270025264 bp After Masking: 161827904 bp Masked: 40.07 % -- Input Database Coverage: 400058109 bp out of 2633804377 bp ( 15.19 % ) Sampling Time: 00:24:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 08:11:35 (hh:mm:ss) Elapsed Time, 1096972 HSPs Collected Number of families returned by RECON: 33142 Round Time: 08:44:03 (hh:mm:ss) Elapsed Time : 333 families discovered. RepeatScout/RECON discovery complete: 751 families found Classification Time: 00:14:18 (hh:mm:ss) Elapsed Time Program Time: 10:45:29 (hh:mm:ss) Elapsed Time