RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ixvrXy/RM_3933155.SunFeb232317012025 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: 1740381420 Database = /dev/shm/rModeler.ixvrXy/GCA_965152275.1_rNatDep2.hap1 - Sequences = 41 - Bases = 2173446978 Storage Throughput = excellent ( 1813.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002781 bp ( 40001881 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:17 (hh:mm:ss) Elapsed Time Round Time: 00:10:37 (hh:mm:ss) Elapsed Time : 543 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 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13470 repeats masked totaling 3066973 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000720 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10000320 bp After Masking: 6835173 bp Masked: 31.65 % -- Input Database Coverage: 10000720 bp out of 2173446978 bp ( 0.46 % ) Sampling Time: 00:00:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:54 (hh:mm:ss) Elapsed Time, 13298 HSPs Collected Number of families returned by RECON: 1662 Round Time: 00:03:47 (hh:mm:ss) Elapsed Time : 32 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44070 repeats masked totaling 9626974 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001981 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30001481 bp After Masking: 20087451 bp Masked: 33.05 % -- Input Database Coverage: 40002701 bp out of 2173446978 bp ( 1.84 % ) Sampling Time: 00:02:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:12:27 (hh:mm:ss) Elapsed Time, 57062 HSPs Collected Number of families returned by RECON: 4904 Round Time: 00:15:15 (hh:mm:ss) Elapsed Time : 129 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 154881 repeats masked totaling 32098137 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90007186 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90005886 bp After Masking: 57104475 bp Masked: 36.55 % -- Input Database Coverage: 130009887 bp out of 2173446978 bp ( 5.98 % ) Sampling Time: 00:05:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:05:57 (hh:mm:ss) Elapsed Time, 238770 HSPs Collected Number of families returned by RECON: 13985 Round Time: 01:16:19 (hh:mm:ss) Elapsed Time : 465 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 533922 repeats masked totaling 112568219 bp(s). - TE Masking time 00:03:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270011162 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 270006562 bp After Masking: 155422647 bp Masked: 42.44 % -- Input Database Coverage: 400021049 bp out of 2173446978 bp ( 18.40 % ) Sampling Time: 00:19:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 06:56:06 (hh:mm:ss) Elapsed Time, 672909 HSPs Collected Number of families returned by RECON: 44387 Round Time: 07:39:27 (hh:mm:ss) Elapsed Time : 1011 families discovered. RepeatScout/RECON discovery complete: 2180 families found Classification Time: 00:43:07 (hh:mm:ss) Elapsed Time Program Time: 10:08:32 (hh:mm:ss) Elapsed Time