RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.zDjQD7/RM_2386550.SatApr120909102025 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: 1744474149 Database = /data/tmp/rModeler.zDjQD7/GCA_964271855.1_mAcoMin1 - Sequences = 113 - Bases = 2350237540 - N50 = 127517683 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 175191450-187704340 | [ 1 ] 162678561-175191450 | [ ] 150165672-162678561 | [ ] 137652782-150165671 |* [ 2 ] 125139893-137652782 |** [ 5 ] 112627004-125139893 |*** [ 6 ] 100114114-112627003 | [ 1 ] 87601225-100114114 | [ 1 ] 75088336-87601225 | [ ] 62575446-75088335 |* [ 3 ] 50062557-62575446 | [ ] 37549668-50062557 | [ ] 25036778-37549667 | [ 1 ] 12523889-25036778 | [ ] 11000-12523889 |************************************************** [ 93 ] Storage Throughput = excellent ( 1540.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032343 bp ( 40032043 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:20 (hh:mm:ss) Elapsed Time Round Time: 00:12:12 (hh:mm:ss) Elapsed Time : 244 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 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14610 repeats masked totaling 2026809 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037833 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10037833 bp After Masking: 7536179 bp Masked: 24.92 % -- Input Database Coverage: 10037833 bp out of 2350237540 bp ( 0.43 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:25 (hh:mm:ss) Elapsed Time, 34201 HSPs Collected Number of families returned by RECON: 940 Round Time: 00:05:26 (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 : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46574 repeats masked totaling 7510957 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034354 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30034054 bp After Masking: 20657938 bp Masked: 31.22 % -- Input Database Coverage: 40072187 bp out of 2350237540 bp ( 1.71 % ) Sampling Time: 00:02:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:15:24 (hh:mm:ss) Elapsed Time, 44888 HSPs Collected Number of families returned by RECON: 2493 Round Time: 00:18:39 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 150605 repeats masked totaling 24329306 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012443 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 90011743 bp After Masking: 60434927 bp Masked: 32.86 % -- Input Database Coverage: 130084630 bp out of 2350237540 bp ( 5.53 % ) Sampling Time: 00:06:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:33:17 (hh:mm:ss) Elapsed Time, 101881 HSPs Collected Number of families returned by RECON: 8682 Round Time: 01:42:06 (hh:mm:ss) Elapsed Time : 180 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 508725 repeats masked totaling 82318798 bp(s). - TE Masking time 00:03:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023180 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 270021147 bp After Masking: 172065715 bp Masked: 36.28 % -- Input Database Coverage: 400107810 bp out of 2350237540 bp ( 17.02 % ) Sampling Time: 00:22:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 10:48:18 (hh:mm:ss) Elapsed Time, 227491 HSPs Collected Number of families returned by RECON: 34824 Round Time: 11:21:55 (hh:mm:ss) Elapsed Time : 382 families discovered. RepeatScout/RECON discovery complete: 890 families found Classification Time: 00:19:24 (hh:mm:ss) Elapsed Time Program Time: 13:59:42 (hh:mm:ss) Elapsed Time