RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.d0OqaV/RM_78376.SunJan210029212024 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: 1705825761 Database = /dev/shm/rModeler.d0OqaV/GCA_028885685.2_NHGRI_mPonAbe1-v2.0_alt - Sequences = 48 - Bases = 3000996708 Storage Throughput = excellent ( 1166.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40133836 bp ( 40013823 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:42 (hh:mm:ss) Elapsed Time Round Time: 00:24:49 (hh:mm:ss) Elapsed Time : 259 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11516 repeats masked totaling 2816547 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040242 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10000232 bp After Masking: 5911754 bp Masked: 40.88 % -- Input Database Coverage: 10040242 bp out of 3000996708 bp ( 0.33 % ) Sampling Time: 00:03:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:17 (hh:mm:ss) Elapsed Time, 5318 HSPs Collected Number of families returned by RECON: 880 Round Time: 00:09:03 (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 : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37770 repeats masked totaling 9291334 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30093514 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30013511 bp After Masking: 18406542 bp Masked: 38.67 % -- Input Database Coverage: 40133756 bp out of 3000996708 bp ( 1.34 % ) Sampling Time: 00:06:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:25:32 (hh:mm:ss) Elapsed Time, 28020 HSPs Collected Number of families returned by RECON: 2291 Round Time: 00:32:40 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 125592 repeats masked totaling 30899613 bp(s). - TE Masking time 00:01:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90235781 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90035770 bp After Masking: 52415240 bp Masked: 41.78 % -- Input Database Coverage: 130369537 bp out of 3000996708 bp ( 4.34 % ) Sampling Time: 00:25:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 02:30:17 (hh:mm:ss) Elapsed Time, 99998 HSPs Collected Number of families returned by RECON: 7748 Round Time: 02:59:42 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:52:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 415358 repeats masked totaling 102183763 bp(s). - TE Masking time 00:05:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270676643 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 270020575 bp After Masking: 148437843 bp Masked: 45.03 % -- Input Database Coverage: 401046180 bp out of 3000996708 bp ( 13.36 % ) Sampling Time: 01:11:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 17:50:33 (hh:mm:ss) Elapsed Time, 331800 HSPs Collected Number of families returned by RECON: 29233 Round Time: 19:18:23 (hh:mm:ss) Elapsed Time : 434 families discovered. RepeatScout/RECON discovery complete: 951 families found Classification Time: 00:33:53 (hh:mm:ss) Elapsed Time Program Time: 23:58:30 (hh:mm:ss) Elapsed Time