RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.qHk56m/RM_78561.SunJan210031062024 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: 1705825865 Database = /dev/shm/rModeler.qHk56m/GCA_028878085.2_NHGRI_mSymSyn1-v2.0_alt - Sequences = 40 - Bases = 3097367794 Storage Throughput = excellent ( 1489.76 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005796 bp ( 40005796 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:15 (hh:mm:ss) Elapsed Time Round Time: 00:36:19 (hh:mm:ss) Elapsed Time : 237 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11558 repeats masked totaling 2772224 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000288 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000288 bp After Masking: 5719089 bp Masked: 42.81 % -- Input Database Coverage: 10000288 bp out of 3097367794 bp ( 0.32 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:03 (hh:mm:ss) Elapsed Time, 5485 HSPs Collected Number of families returned by RECON: 749 Round Time: 00:06:36 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41189 repeats masked totaling 9854034 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005428 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30005428 bp After Masking: 16614338 bp Masked: 44.63 % -- Input Database Coverage: 40005716 bp out of 3097367794 bp ( 1.29 % ) Sampling Time: 00:03:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:23:12 (hh:mm:ss) Elapsed Time, 22253 HSPs Collected Number of families returned by RECON: 1981 Round Time: 00:27:36 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 124292 repeats masked totaling 29909640 bp(s). - TE Masking time 00:01:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044678 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 90004676 bp After Masking: 47346041 bp Masked: 47.40 % -- Input Database Coverage: 130050394 bp out of 3097367794 bp ( 4.20 % ) Sampling Time: 00:10:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:14:18 (hh:mm:ss) Elapsed Time, 77285 HSPs Collected Number of families returned by RECON: 6418 Round Time: 02:27:42 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 405675 repeats masked totaling 97986456 bp(s). - TE Masking time 00:06:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270156475 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 270000083 bp After Masking: 136696795 bp Masked: 49.37 % -- Input Database Coverage: 400206869 bp out of 3097367794 bp ( 12.92 % ) Sampling Time: 00:34:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 15:48:18 (hh:mm:ss) Elapsed Time, 222586 HSPs Collected Number of families returned by RECON: 25696 Round Time: 16:38:22 (hh:mm:ss) Elapsed Time : 375 families discovered. RepeatScout/RECON discovery complete: 855 families found Classification Time: 00:43:42 (hh:mm:ss) Elapsed Time Program Time: 21:00:17 (hh:mm:ss) Elapsed Time