RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.imynbl/RM_7642.WedJan101935342024 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: 1704944134 Database = /dev/shm/rModeler.imynbl/GCA_011762515.1_mTurTru1.pat - Sequences = 1166 - Bases = 2378995196 - N50 = 88769969 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 171716131-183981498 | [ 1 ] 159450765-171716131 | [ ] 147185399-159450765 | [ 1 ] 134920032-147185398 | [ ] 122654666-134920032 | [ ] 110389300-122654666 | [ 1 ] 98123934-110389300 | [ 5 ] 85858567-98123933 | [ 4 ] 73593201-85858567 | [ 6 ] 61327835-73593201 | [ ] 49062469-61327835 | [ 2 ] 36797102-49062468 | [ 2 ] 24531736-36797102 | [ 5 ] 12266370-24531736 | [ 4 ] 1004-12266370 |************************************************** [ 1135 ] Storage Throughput = excellent ( 1124.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40964987 bp ( 40004535 non ambiguous ) - Num Contigs Represented = 83 - Sequence extraction : 00:01:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:14 (hh:mm:ss) Elapsed Time Round Time: 00:32:05 (hh:mm:ss) Elapsed Time : 216 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (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... 10584 repeats masked totaling 2688196 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10252937 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10009417 bp After Masking: 7277448 bp Masked: 27.29 % -- Input Database Coverage: 10252937 bp out of 2378995196 bp ( 0.43 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:05:30 (hh:mm:ss) Elapsed Time, 7376 HSPs Collected Number of families returned by RECON: 911 Round Time: 00:06:53 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33721 repeats masked totaling 8881090 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30751966 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 30035034 bp After Masking: 21003971 bp Masked: 30.07 % -- Input Database Coverage: 41004903 bp out of 2378995196 bp ( 1.72 % ) Sampling Time: 00:03:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 300700 Comparison Time: 00:29:05 (hh:mm:ss) Elapsed Time, 25097 HSPs Collected Number of families returned by RECON: 2645 Round Time: 00:33:11 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107180 repeats masked totaling 29292426 bp(s). - TE Masking time 00:01:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91342011 bp Num Contigs Represented = 135 Non ambiguous bp: Initial: 90014537 bp After Masking: 60292451 bp Masked: 33.02 % -- Input Database Coverage: 132346914 bp out of 2378995196 bp ( 5.56 % ) Sampling Time: 00:10:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2673828 Comparison Time: 03:25:54 (hh:mm:ss) Elapsed Time, 91378 HSPs Collected Number of families returned by RECON: 9461 Round Time: 03:41:09 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 368831 repeats masked totaling 97931461 bp(s). - TE Masking time 00:06:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 276129645 bp Num Contigs Represented = 264 Non ambiguous bp: Initial: 270004856 bp After Masking: 170731902 bp Masked: 36.77 % -- Input Database Coverage: 408476559 bp out of 2378995196 bp ( 17.17 % ) Sampling Time: 00:33:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24426555 Comparison Time: 26:21:31 (hh:mm:ss) Elapsed Time, 206112 HSPs Collected Number of families returned by RECON: 36159 Round Time: 27:26:44 (hh:mm:ss) Elapsed Time : 362 families discovered. RepeatScout/RECON discovery complete: 860 families found Classification Time: 00:32:44 (hh:mm:ss) Elapsed Time Program Time: 32:52:46 (hh:mm:ss) Elapsed Time