RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.eUZBcU/RM_87937.FriFeb71208012025 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: 1738958877 Database = /data/tmp/rModeler.eUZBcU/GCA_045345505.1_bMorGui1_haplotype_1 - Sequences = 548 - Bases = 1316595704 - N50 = 60943587 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 80739987-86506496 | [ 4 ] 74973479-80739987 | [ ] 69206970-74973478 | [ 2 ] 63440462-69206970 | [ 1 ] 57673954-63440462 | [ 2 ] 51907445-57673953 | [ 1 ] 46140937-51907445 | [ 2 ] 40374428-46140936 | [ 4 ] 34607920-40374428 | [ 1 ] 28841412-34607920 | [ 2 ] 23074903-28841411 | [ 4 ] 17308395-23074903 | [ ] 11541886-17308394 | [ ] 5775378-11541886 | [ 3 ] 8870-5775378 |************************************************** [ 522 ] Storage Throughput = excellent ( 1421.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015451 bp ( 40014451 non ambiguous ) - Num Contigs Represented = 88 - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:34 (hh:mm:ss) Elapsed Time Round Time: 00:21:11 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1401 repeats masked totaling 701820 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020134 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10019734 bp After Masking: 8569730 bp Masked: 14.47 % -- Input Database Coverage: 10020134 bp out of 1316595704 bp ( 0.76 % ) Sampling Time: 00:04:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:18 (hh:mm:ss) Elapsed Time, 4053 HSPs Collected Number of families returned by RECON: 255 Round Time: 00:07:26 (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 : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4465 repeats masked totaling 2398732 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031721 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 30031121 bp After Masking: 24080967 bp Masked: 19.81 % -- Input Database Coverage: 40051855 bp out of 1316595704 bp ( 3.04 % ) Sampling Time: 00:11:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:16:36 (hh:mm:ss) Elapsed Time, 185554 HSPs Collected Number of families returned by RECON: 1292 Round Time: 00:33:05 (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 : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13978 repeats masked totaling 6665480 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016614 bp Num Contigs Represented = 141 Non ambiguous bp: Initial: 90015414 bp After Masking: 73678095 bp Masked: 18.15 % -- Input Database Coverage: 130068469 bp out of 1316595704 bp ( 9.88 % ) Sampling Time: 00:39:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 01:45:42 (hh:mm:ss) Elapsed Time, 227811 HSPs Collected Number of families returned by RECON: 7707 Round Time: 02:27:31 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:52:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54564 repeats masked totaling 24658416 bp(s). - TE Masking time 00:02:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270021596 bp Num Contigs Represented = 246 Non ambiguous bp: Initial: 270016996 bp After Masking: 216681209 bp Masked: 19.75 % -- Input Database Coverage: 400090065 bp out of 1316595704 bp ( 30.39 % ) Sampling Time: 01:59:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23143806 Comparison Time: 15:34:41 (hh:mm:ss) Elapsed Time, 2831922 HSPs Collected Number of families returned by RECON: 47387 Round Time: 17:54:14 (hh:mm:ss) Elapsed Time : 215 families discovered. RepeatScout/RECON discovery complete: 377 families found Classification Time: 00:25:25 (hh:mm:ss) Elapsed Time Program Time: 21:48:52 (hh:mm:ss) Elapsed Time