RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.J3YuOA/RM_2345304.SunApr200307122025 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: 1745143632 Database = /data/tmp/rModeler.J3YuOA/GCF_042477335.2_ARS-UI_OviCan_v2 - Sequences = 42 - Bases = 2974283533 Storage Throughput = excellent ( 1182.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001599 bp ( 40001599 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:07 (hh:mm:ss) Elapsed Time Round Time: 00:26:41 (hh:mm:ss) Elapsed Time : 240 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16088 repeats masked totaling 4028106 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000426 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10000426 bp After Masking: 5935279 bp Masked: 40.65 % -- Input Database Coverage: 10000426 bp out of 2974283533 bp ( 0.34 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:16 (hh:mm:ss) Elapsed Time, 475906 HSPs Collected Number of families returned by RECON: 630 Round Time: 00:15:28 (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 : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51274 repeats masked totaling 12163387 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001170 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30001170 bp After Masking: 17467918 bp Masked: 41.78 % -- Input Database Coverage: 40001596 bp out of 2974283533 bp ( 1.34 % ) Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:26:28 (hh:mm:ss) Elapsed Time, 19137 HSPs Collected Number of families returned by RECON: 1864 Round Time: 00:32:14 (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 : 00:02:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 162891 repeats masked totaling 38919466 bp(s). - TE Masking time 00:01:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038007 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 90038007 bp After Masking: 49899360 bp Masked: 44.58 % -- Input Database Coverage: 130039603 bp out of 2974283533 bp ( 4.37 % ) Sampling Time: 00:09:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:27:22 (hh:mm:ss) Elapsed Time, 65248 HSPs Collected Number of families returned by RECON: 6638 Round Time: 03:26:41 (hh:mm:ss) Elapsed Time : 158 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 526369 repeats masked totaling 124784764 bp(s). - TE Masking time 00:05:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270016047 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 270016047 bp After Masking: 141808647 bp Masked: 47.48 % -- Input Database Coverage: 400055650 bp out of 2974283533 bp ( 13.45 % ) Sampling Time: 00:32:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 18:03:09 (hh:mm:ss) Elapsed Time, 182403 HSPs Collected Number of families returned by RECON: 27133 Round Time: 19:19:58 (hh:mm:ss) Elapsed Time : 333 families discovered. RepeatScout/RECON discovery complete: 803 families found Classification Time: 00:32:01 (hh:mm:ss) Elapsed Time Program Time: 24:33:03 (hh:mm:ss) Elapsed Time