RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ckqTWz/RM_1341449.WedDec181114042024 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: 1734549243 Database = /dev/shm/rModeler.ckqTWz/GCA_964059295.1_bNumArq3.hap2.1 - Sequences = 811 - Bases = 1198356613 - N50 = 70289158 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 132294776-141744332 | [ 2 ] 122845221-132294776 | [ ] 113395665-122845220 | [ ] 103946110-113395665 | [ ] 94496554-103946109 | [ ] 85046999-94496554 | [ ] 75597443-85046998 | [ 2 ] 66147888-75597443 | [ 2 ] 56698332-66147887 | [ 3 ] 47248777-56698332 | [ 1 ] 37799221-47248776 | [ 1 ] 28349666-37799221 | [ ] 18900110-28349665 | [ 3 ] 9450555-18900110 | [ 6 ] 1000-9450555 |************************************************** [ 791 ] Storage Throughput = fair ( 499.44 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40042624 bp ( 40037224 non ambiguous ) - Num Contigs Represented = 132 - Sequence extraction : 00:02:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:38:34 (hh:mm:ss) Elapsed Time Round Time: 01:04:40 (hh:mm:ss) Elapsed Time : 77 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 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6293 repeats masked totaling 1148188 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038319 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 10037119 bp After Masking: 8676529 bp Masked: 13.56 % -- Input Database Coverage: 10038319 bp out of 1198356613 bp ( 0.84 % ) Sampling Time: 00:02:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:15:46 (hh:mm:ss) Elapsed Time, 4146 HSPs Collected Number of families returned by RECON: 247 Round Time: 00:18:30 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17429 repeats masked totaling 3485237 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004293 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 30000093 bp After Masking: 25945295 bp Masked: 13.52 % -- Input Database Coverage: 40042612 bp out of 1198356613 bp ( 3.34 % ) Sampling Time: 00:05:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 01:58:20 (hh:mm:ss) Elapsed Time, 26186 HSPs Collected Number of families returned by RECON: 1367 Round Time: 02:05:54 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43407 repeats masked totaling 9527544 bp(s). - TE Masking time 00:03:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015585 bp Num Contigs Represented = 200 Non ambiguous bp: Initial: 90004585 bp After Masking: 78691638 bp Masked: 12.57 % -- Input Database Coverage: 130058197 bp out of 1198356613 bp ( 10.85 % ) Sampling Time: 00:22:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2609470 Comparison Time: 14:14:39 (hh:mm:ss) Elapsed Time, 69077 HSPs Collected Number of families returned by RECON: 8258 Round Time: 14:46:23 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 135846 repeats masked totaling 32664535 bp(s). - TE Masking time 00:10:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032523 bp Num Contigs Represented = 414 Non ambiguous bp: Initial: 270000123 bp After Masking: 231266808 bp Masked: 14.35 % -- Input Database Coverage: 400090720 bp out of 1198356613 bp ( 33.39 % ) Sampling Time: 00:57:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23416746 Comparison Time: 121:18:02 (hh:mm:ss) Elapsed Time, 679483 HSPs Collected Number of families returned by RECON: 50829 Round Time: 124:43:07 (hh:mm:ss) Elapsed Time : 252 families discovered. RepeatScout/RECON discovery complete: 395 families found Classification Time: 01:29:32 (hh:mm:ss) Elapsed Time Program Time: 144:28:06 (hh:mm:ss) Elapsed Time