RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Dc4mKy/RM_1822.SunJan80216112023 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: 1673172970 Database = /dev/shm/rModeler.Dc4mKy/GCA_020745705.1_bHemCom1.pri.cur - Sequences = 146 - Bases = 1164813063 - N50 = 123375213 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 203847990-218408531 | [ 1 ] 189287449-203847989 | [ ] 174726908-189287448 | [ ] 160166368-174726908 | [ 1 ] 145605827-160166367 | [ ] 131045286-145605826 | [ ] 116484745-131045285 | [ 1 ] 101924205-116484745 | [ ] 87363664-101924204 | [ 1 ] 72803123-87363663 | [ 1 ] 58242582-72803122 | [ 1 ] 43682042-58242582 | [ ] 29121501-43682041 |* [ 3 ] 14560960-29121500 |*** [ 10 ] 420-14560960 |************************************************** [ 127 ] Storage Throughput = good ( 788.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40260723 bp ( 40020080 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:02:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:05 (hh:mm:ss) Elapsed Time Round Time: 00:28:52 (hh:mm:ss) Elapsed Time : 104 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3006 repeats masked totaling 1056307 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026437 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10021782 bp After Masking: 8931378 bp Masked: 10.88 % -- Input Database Coverage: 10026437 bp out of 1164813063 bp ( 0.86 % ) Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:51 (hh:mm:ss) Elapsed Time, 338 HSPs Collected Number of families returned by RECON: 215 Round Time: 00:07:49 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9624 repeats masked totaling 3185677 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30274286 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30038298 bp After Masking: 26744343 bp Masked: 10.97 % -- Input Database Coverage: 40300723 bp out of 1164813063 bp ( 3.46 % ) Sampling Time: 00:02:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:38:49 (hh:mm:ss) Elapsed Time, 4011 HSPs Collected Number of families returned by RECON: 1469 Round Time: 00:41:54 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28673 repeats masked totaling 9720982 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91051774 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 90032206 bp After Masking: 79880108 bp Masked: 11.28 % -- Input Database Coverage: 131352497 bp out of 1164813063 bp ( 11.28 % ) Sampling Time: 00:08:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2598060 Comparison Time: 04:38:09 (hh:mm:ss) Elapsed Time, 38363 HSPs Collected Number of families returned by RECON: 9713 Round Time: 04:48:58 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 94728 repeats masked totaling 30943455 bp(s). - TE Masking time 00:03:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272163737 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 270014234 bp After Masking: 237989529 bp Masked: 11.86 % -- Input Database Coverage: 403516234 bp out of 1164813063 bp ( 34.64 % ) Sampling Time: 00:25:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23300551 Comparison Time: 37:56:01 (hh:mm:ss) Elapsed Time, 164709 HSPs Collected Number of families returned by RECON: 66068 Round Time: 39:17:54 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatScout/RECON discovery complete: 362 families found Classification Time: 00:18:11 (hh:mm:ss) Elapsed Time Program Time: 45:43:38 (hh:mm:ss) Elapsed Time