RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DJjE8J/RM_105383.MonMay80606092023 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: 1683551167 Database = /dev/shm/rModeler.DJjE8J/GCA_026419965.1_mKogBre1_haplotype_1 - Sequences = 580 - Bases = 2555838840 - N50 = 139403296 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 188928309-202422507 | [ 2 ] 175434112-188928309 | [ 2 ] 161939914-175434111 | [ ] 148445717-161939914 | [ 1 ] 134951519-148445716 | [ 2 ] 121457322-134951519 | [ 1 ] 107963124-121457321 | [ 2 ] 94468927-107963124 | [ 3 ] 80974729-94468926 | [ 3 ] 67480532-80974729 | [ 2 ] 53986334-67480531 | [ 2 ] 40492137-53986334 | [ 1 ] 26997939-40492136 | [ ] 13503742-26997939 | [ ] 9545-13503742 |************************************************** [ 559 ] Storage Throughput = excellent ( 1609.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020368 bp ( 40019842 non ambiguous ) - Num Contigs Represented = 67 - Sequence extraction : 00:01:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:28 (hh:mm:ss) Elapsed Time Round Time: 00:23:26 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (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... 10987 repeats masked totaling 3258868 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020750 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10020737 bp After Masking: 6603189 bp Masked: 34.10 % -- Input Database Coverage: 10020750 bp out of 2555838840 bp ( 0.39 % ) Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:10:25 (hh:mm:ss) Elapsed Time, 11605 HSPs Collected Number of families returned by RECON: 662 Round Time: 00:11:58 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36986 repeats masked totaling 10890641 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039614 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30039101 bp After Masking: 18578196 bp Masked: 38.15 % -- Input Database Coverage: 40060364 bp out of 2555838840 bp ( 1.57 % ) Sampling Time: 00:03:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:37:52 (hh:mm:ss) Elapsed Time, 36437 HSPs Collected Number of families returned by RECON: 1926 Round Time: 00:41:49 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:09 (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... 118173 repeats masked totaling 32568036 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90168576 bp Num Contigs Represented = 85 Non ambiguous bp: Initial: 90006279 bp After Masking: 55926074 bp Masked: 37.86 % -- Input Database Coverage: 130228940 bp out of 2555838840 bp ( 5.10 % ) Sampling Time: 00:08:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 02:36:18 (hh:mm:ss) Elapsed Time, 383353 HSPs Collected Number of families returned by RECON: 7046 Round Time: 02:48:36 (hh:mm:ss) Elapsed Time : 146 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 385168 repeats masked totaling 106075867 bp(s). - TE Masking time 00:04:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270627333 bp Num Contigs Represented = 141 Non ambiguous bp: Initial: 270023157 bp After Masking: 159413701 bp Masked: 40.96 % -- Input Database Coverage: 400856273 bp out of 2555838840 bp ( 15.68 % ) Sampling Time: 00:31:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23028291 Comparison Time: 14:32:27 (hh:mm:ss) Elapsed Time, 5697889 HSPs Collected Number of families returned by RECON: 30526 Round Time: 15:19:31 (hh:mm:ss) Elapsed Time : 344 families discovered. RepeatScout/RECON discovery complete: 759 families found Classification Time: 00:23:46 (hh:mm:ss) Elapsed Time Program Time: 19:49:06 (hh:mm:ss) Elapsed Time