RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MO2Boz/RM_2557209.FriJul190818582024 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: 1721402333 Database = /dev/shm/rModeler.MO2Boz/GCF_023856365.1_BBRACH_0.4 - Sequences = 1425 - Bases = 988088817 - N50 = 27905563 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 52957898-56739146 | [ 1 ] 49176650-52957897 | [ 1 ] 45395402-49176649 | [ ] 41614155-45395402 | [ 1 ] 37832907-41614154 | [ 1 ] 34051659-37832906 | [ 1 ] 30270411-34051658 | [ 3 ] 26489164-30270411 | [ 6 ] 22707916-26489163 | [ 4 ] 18926668-22707915 | [ 5 ] 15145420-18926667 | [ ] 11364173-15145420 | [ 1 ] 7582925-11364172 | [ 1 ] 3801677-7582924 | [ 8 ] 20430-3801677 |************************************************** [ 1392 ] Storage Throughput = fair ( 684.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037049 bp ( 40032549 non ambiguous ) - Num Contigs Represented = 237 - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:25 (hh:mm:ss) Elapsed Time Round Time: 00:40:33 (hh:mm:ss) Elapsed Time : 414 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8392 repeats masked totaling 2622618 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009746 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 10007746 bp After Masking: 6782245 bp Masked: 32.23 % -- Input Database Coverage: 10009746 bp out of 988088817 bp ( 1.01 % ) Sampling Time: 00:03:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:19:59 (hh:mm:ss) Elapsed Time, 5310 HSPs Collected Number of families returned by RECON: 823 Round Time: 00:23:48 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26638 repeats masked totaling 8258637 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027285 bp Num Contigs Represented = 195 Non ambiguous bp: Initial: 30024785 bp After Masking: 19883323 bp Masked: 33.78 % -- Input Database Coverage: 40037031 bp out of 988088817 bp ( 4.05 % ) Sampling Time: 00:07:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 299925 Comparison Time: 01:09:20 (hh:mm:ss) Elapsed Time, 30388 HSPs Collected Number of families returned by RECON: 3018 Round Time: 01:18:48 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86197 repeats masked totaling 25779378 bp(s). - TE Masking time 00:02:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018411 bp Num Contigs Represented = 411 Non ambiguous bp: Initial: 90008911 bp After Masking: 58647497 bp Masked: 34.84 % -- Input Database Coverage: 130055442 bp out of 988088817 bp ( 13.16 % ) Sampling Time: 00:21:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2690040 Comparison Time: 05:32:28 (hh:mm:ss) Elapsed Time, 317057 HSPs Collected Number of families returned by RECON: 10356 Round Time: 06:08:20 (hh:mm:ss) Elapsed Time : 362 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:56:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 299794 repeats masked totaling 90399925 bp(s). - TE Masking time 00:11:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270060294 bp Num Contigs Represented = 840 Non ambiguous bp: Initial: 270031850 bp After Masking: 162739850 bp Masked: 39.73 % -- Input Database Coverage: 400115736 bp out of 988088817 bp ( 40.49 % ) Sampling Time: 01:12:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24217320 Comparison Time: 21:57:08 (hh:mm:ss) Elapsed Time, 983654 HSPs Collected Number of families returned by RECON: 35131 Round Time: 23:47:25 (hh:mm:ss) Elapsed Time : 885 families discovered. RepeatScout/RECON discovery complete: 1743 families found Classification Time: 01:55:49 (hh:mm:ss) Elapsed Time Program Time: 34:14:43 (hh:mm:ss) Elapsed Time