RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ZhUdNr/RM_307565.FriJan191009392024 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: 1705687774 Database = /dev/shm/rModeler.ZhUdNr/GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri - Sequences = 26 - Bases = 3262887708 Storage Throughput = good ( 775.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041271 bp ( 40001265 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:50 (hh:mm:ss) Elapsed Time Round Time: 00:41:52 (hh:mm:ss) Elapsed Time : 224 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10062 repeats masked totaling 2903110 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040382 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10000376 bp After Masking: 5884688 bp Masked: 41.16 % -- Input Database Coverage: 10040382 bp out of 3262887708 bp ( 0.31 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:27:34 (hh:mm:ss) Elapsed Time, 8482 HSPs Collected Number of families returned by RECON: 886 Round Time: 00:30:34 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38111 repeats masked totaling 9761467 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000886 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30000886 bp After Masking: 15935086 bp Masked: 46.88 % -- Input Database Coverage: 40041268 bp out of 3262887708 bp ( 1.23 % ) Sampling Time: 00:03:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 02:25:59 (hh:mm:ss) Elapsed Time, 21685 HSPs Collected Number of families returned by RECON: 1945 Round Time: 02:31:03 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118851 repeats masked totaling 30325874 bp(s). - TE Masking time 00:02:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003182 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90003182 bp After Masking: 47780760 bp Masked: 46.91 % -- Input Database Coverage: 130044450 bp out of 3262887708 bp ( 3.99 % ) Sampling Time: 00:11:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 05:05:30 (hh:mm:ss) Elapsed Time, 94897 HSPs Collected Number of families returned by RECON: 6992 Round Time: 05:21:10 (hh:mm:ss) Elapsed Time : 168 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 397354 repeats masked totaling 99583315 bp(s). - TE Masking time 00:06:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270053320 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270013314 bp After Masking: 137730359 bp Masked: 48.99 % -- Input Database Coverage: 400097770 bp out of 3262887708 bp ( 12.26 % ) Sampling Time: 00:34:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 17:31:08 (hh:mm:ss) Elapsed Time, 320819 HSPs Collected Number of families returned by RECON: 26894 Round Time: 18:27:07 (hh:mm:ss) Elapsed Time : 398 families discovered. RepeatScout/RECON discovery complete: 860 families found Classification Time: 00:50:45 (hh:mm:ss) Elapsed Time Program Time: 28:22:31 (hh:mm:ss) Elapsed Time