RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.SgFf7h/RM_3234213.MonApr140654392025 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: 1744638879 Database = /data/tmp/rModeler.SgFf7h/GCA_044231665.1_SynOce1_v1.hap1 - Sequences = 107 - Bases = 470091028 - N50 = 23573699 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 34728595-37209138 | [ 1 ] 32248052-34728594 |* [ 2 ] 29767510-32248052 |* [ 2 ] 27286967-29767509 | [ ] 24806425-27286967 | [ ] 22325882-24806424 |* [ 3 ] 19845340-22325882 |*** [ 6 ] 17364797-19845339 |* [ 2 ] 14884255-17364797 |** [ 4 ] 12403712-14884254 | [ ] 9923170-12403712 | [ ] 7442627-9923169 | [ ] 4962085-7442627 | [ ] 2481542-4962084 | [ ] 1000-2481542 |************************************************** [ 87 ] Storage Throughput = excellent ( 1687.59 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019757 bp ( 40019257 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:51 (hh:mm:ss) Elapsed Time Round Time: 00:13:32 (hh:mm:ss) Elapsed Time : 287 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (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... 5841 repeats masked totaling 875572 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004588 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10004488 bp After Masking: 8942092 bp Masked: 10.62 % -- Input Database Coverage: 10004588 bp out of 470091028 bp ( 2.13 % ) Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:37 (hh:mm:ss) Elapsed Time, 5259 HSPs Collected Number of families returned by RECON: 1093 Round Time: 00:04:10 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19245 repeats masked totaling 2912200 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015128 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30014728 bp After Masking: 26142319 bp Masked: 12.90 % -- Input Database Coverage: 40019716 bp out of 470091028 bp ( 8.51 % ) Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:17:59 (hh:mm:ss) Elapsed Time, 35165 HSPs Collected Number of families returned by RECON: 4175 Round Time: 00:20:02 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 69764 repeats masked totaling 10402176 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003310 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90001810 bp After Masking: 77183750 bp Masked: 14.24 % -- Input Database Coverage: 130023026 bp out of 470091028 bp ( 27.66 % ) Sampling Time: 00:03:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:39:17 (hh:mm:ss) Elapsed Time, 178674 HSPs Collected Number of families returned by RECON: 15666 Round Time: 01:47:40 (hh:mm:ss) Elapsed Time : 334 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 258248 repeats masked totaling 39864230 bp(s). - TE Masking time 00:03:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032186 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 270026386 bp After Masking: 222098130 bp Masked: 17.75 % -- Input Database Coverage: 400055212 bp out of 470091028 bp ( 85.10 % ) Sampling Time: 00:14:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 12:49:03 (hh:mm:ss) Elapsed Time, 434854 HSPs Collected Number of families returned by RECON: 61461 Round Time: 13:34:21 (hh:mm:ss) Elapsed Time : 738 families discovered. RepeatScout/RECON discovery complete: 1464 families found Classification Time: 00:34:56 (hh:mm:ss) Elapsed Time Program Time: 16:34:41 (hh:mm:ss) Elapsed Time