RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.coCMaR/RM_307519.FriJan191009262024 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: 1705687759 Database = /dev/shm/rModeler.coCMaR/GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri - Sequences = 29 - Bases = 3259853530 Storage Throughput = fair ( 673.73 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40236098 bp ( 40036082 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:17 (hh:mm:ss) Elapsed Time Round Time: 00:30:32 (hh:mm:ss) Elapsed Time : 252 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13946 repeats masked totaling 2866524 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040175 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000170 bp After Masking: 6163831 bp Masked: 38.36 % -- Input Database Coverage: 10040175 bp out of 3259853530 bp ( 0.31 % ) Sampling Time: 00:03:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:31:01 (hh:mm:ss) Elapsed Time, 6600 HSPs Collected Number of families returned by RECON: 875 Round Time: 00:35:37 (hh:mm:ss) Elapsed Time : 21 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 00:11:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44386 repeats masked totaling 9438420 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30195843 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30035832 bp After Masking: 17267331 bp Masked: 42.51 % -- Input Database Coverage: 40236018 bp out of 3259853530 bp ( 1.23 % ) Sampling Time: 00:12:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 02:25:35 (hh:mm:ss) Elapsed Time, 27353 HSPs Collected Number of families returned by RECON: 2073 Round Time: 02:40:37 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149896 repeats masked totaling 30865523 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90239549 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90011431 bp After Masking: 50946149 bp Masked: 43.40 % -- Input Database Coverage: 130475567 bp out of 3259853530 bp ( 4.00 % ) Sampling Time: 00:30:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 04:56:30 (hh:mm:ss) Elapsed Time, 98375 HSPs Collected Number of families returned by RECON: 7405 Round Time: 05:30:11 (hh:mm:ss) Elapsed Time : 188 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:20:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 482045 repeats masked totaling 101499917 bp(s). - TE Masking time 00:04:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270671274 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270002144 bp After Masking: 142769261 bp Masked: 47.12 % -- Input Database Coverage: 401146841 bp out of 3259853530 bp ( 12.31 % ) Sampling Time: 01:36:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22906296 Comparison Time: 18:21:46 (hh:mm:ss) Elapsed Time, 261525 HSPs Collected Number of families returned by RECON: 28278 Round Time: 20:23:12 (hh:mm:ss) Elapsed Time : 405 families discovered. RepeatScout/RECON discovery complete: 937 families found Classification Time: 00:38:21 (hh:mm:ss) Elapsed Time Program Time: 30:18:30 (hh:mm:ss) Elapsed Time