RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rC8RHo/RM_439606.SunJul201905252025 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: 1753063524 Database = /dev/shm/rModeler.rC8RHo/GCA_965204225.1_mPipPip2.hap2.1 - Sequences = 369 - Bases = 1854961430 - N50 = 98596842 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 191753792-205450420 | [ 2 ] 178057164-191753792 | [ 1 ] 164360536-178057164 | [ ] 150663908-164360536 | [ ] 136967280-150663908 | [ ] 123270652-136967280 | [ ] 109574024-123270652 | [ ] 95877396-109574024 | [ 3 ] 82180768-95877396 | [ 3 ] 68484140-82180768 | [ 3 ] 54787512-68484140 | [ 1 ] 41090884-54787512 | [ 5 ] 27394256-41090884 | [ 1 ] 13697628-27394256 | [ 3 ] 1000-13697628 |************************************************** [ 347 ] Storage Throughput = excellent ( 1711.70 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40044493 bp ( 40036893 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:09 (hh:mm:ss) Elapsed Time Round Time: 00:10:51 (hh:mm:ss) Elapsed Time : 319 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 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13897 repeats masked totaling 2339701 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035006 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10033406 bp After Masking: 7269582 bp Masked: 27.55 % -- Input Database Coverage: 10035006 bp out of 1854961430 bp ( 0.54 % ) Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:54 (hh:mm:ss) Elapsed Time, 5077 HSPs Collected Number of families returned by RECON: 871 Round Time: 00:03:36 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43991 repeats masked totaling 7360413 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009407 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30003407 bp After Masking: 21255247 bp Masked: 29.16 % -- Input Database Coverage: 40044413 bp out of 1854961430 bp ( 2.16 % ) Sampling Time: 00:02:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:13:03 (hh:mm:ss) Elapsed Time, 177805 HSPs Collected Number of families returned by RECON: 2602 Round Time: 00:15:48 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 142149 repeats masked totaling 23962776 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042150 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 90026101 bp After Masking: 62634228 bp Masked: 30.43 % -- Input Database Coverage: 130086563 bp out of 1854961430 bp ( 7.01 % ) Sampling Time: 00:05:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:17:37 (hh:mm:ss) Elapsed Time, 1274741 HSPs Collected Number of families returned by RECON: 8354 Round Time: 01:24:52 (hh:mm:ss) Elapsed Time : 212 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 465063 repeats masked totaling 79572813 bp(s). - TE Masking time 00:02:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270051309 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 270005068 bp After Masking: 180490328 bp Masked: 33.15 % -- Input Database Coverage: 400137872 bp out of 1854961430 bp ( 21.57 % ) Sampling Time: 00:17:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 09:19:00 (hh:mm:ss) Elapsed Time, 6863710 HSPs Collected Number of families returned by RECON: 36687 Round Time: 09:48:09 (hh:mm:ss) Elapsed Time : 424 families discovered. RepeatScout/RECON discovery complete: 1037 families found Classification Time: 00:17:22 (hh:mm:ss) Elapsed Time Program Time: 12:00:38 (hh:mm:ss) Elapsed Time