RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.haZfQc/RM_31901.TueJun252041582024 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: 1719373318 Database = /dev/shm/rModeler.haZfQc/GCF_028858775.2_NHGRI_mPanTro3-v2.0_pri - Sequences = 26 - Bases = 3177756316 Storage Throughput = excellent ( 1043.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001547 bp ( 40001547 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:49 (hh:mm:ss) Elapsed Time Round Time: 00:32:50 (hh:mm:ss) Elapsed Time : 234 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11992 repeats masked totaling 2779307 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000236 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000236 bp After Masking: 5904079 bp Masked: 40.96 % -- Input Database Coverage: 10000236 bp out of 3177756316 bp ( 0.31 % ) Sampling Time: 00:03:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:48 (hh:mm:ss) Elapsed Time, 5920 HSPs Collected Number of families returned by RECON: 790 Round Time: 00:08:14 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39915 repeats masked totaling 9407342 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001231 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30001231 bp After Masking: 17780766 bp Masked: 40.73 % -- Input Database Coverage: 40001467 bp out of 3177756316 bp ( 1.26 % ) Sampling Time: 00:09:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:25:33 (hh:mm:ss) Elapsed Time, 28377 HSPs Collected Number of families returned by RECON: 2347 Round Time: 00:35:48 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 126689 repeats masked totaling 30324633 bp(s). - TE Masking time 00:01:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90168131 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90008125 bp After Masking: 51380628 bp Masked: 42.92 % -- Input Database Coverage: 130169598 bp out of 3177756316 bp ( 4.10 % ) Sampling Time: 00:26:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 02:50:44 (hh:mm:ss) Elapsed Time, 96030 HSPs Collected Number of families returned by RECON: 7239 Round Time: 03:22:52 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:03:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 413783 repeats masked totaling 98218757 bp(s). - TE Masking time 00:07:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270530631 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270010595 bp After Masking: 145279487 bp Masked: 46.19 % -- Input Database Coverage: 400700229 bp out of 3177756316 bp ( 12.61 % ) Sampling Time: 01:22:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 21:52:35 (hh:mm:ss) Elapsed Time, 263130 HSPs Collected Number of families returned by RECON: 29039 Round Time: 23:42:25 (hh:mm:ss) Elapsed Time : 395 families discovered. RepeatScout/RECON discovery complete: 897 families found Classification Time: 00:42:28 (hh:mm:ss) Elapsed Time Program Time: 29:04:38 (hh:mm:ss) Elapsed Time