RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.1CsbE6/RM_456577.SunMay140024242023 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: 1684049064 Database = /dev/shm/rModeler.1CsbE6/GCA_901000725.3_fTakRub1.3 - Sequences = 128 - Bases = 384126663 - N50 = 16842301 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 27284512-29232231 | [ 1 ] 25336793-27284511 | [ ] 23389074-25336792 | [ ] 21441355-23389073 | [ 1 ] 19493636-21441354 | [ 2 ] 17545917-19493635 | [ 2 ] 15598198-17545916 |**** [ 9 ] 13650480-15598198 | [ 2 ] 11702761-13650479 |* [ 4 ] 9755042-11702760 | [ 1 ] 7807323-9755041 | [ ] 5859604-7807322 | [ ] 3911885-5859603 | [ ] 1964166-3911884 | [ ] 16448-1964166 |************************************************** [ 106 ] Storage Throughput = excellent ( 1162.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40353719 bp ( 40026796 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:58 (hh:mm:ss) Elapsed Time Round Time: 00:18:42 (hh:mm:ss) Elapsed Time : 174 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (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... 2308 repeats masked totaling 778859 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10043139 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10002404 bp After Masking: 8758100 bp Masked: 12.44 % -- Input Database Coverage: 10043139 bp out of 384126663 bp ( 2.61 % ) Sampling Time: 00:01:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:53 (hh:mm:ss) Elapsed Time, 2176 HSPs Collected Number of families returned by RECON: 632 Round Time: 00:08:29 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7099 repeats masked totaling 2389356 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30310560 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30024372 bp After Masking: 26371037 bp Masked: 12.17 % -- Input Database Coverage: 40353699 bp out of 384126663 bp ( 10.51 % ) Sampling Time: 00:03:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:32:14 (hh:mm:ss) Elapsed Time, 17271 HSPs Collected Number of families returned by RECON: 3062 Round Time: 00:36:14 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22169 repeats masked totaling 6936737 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90900591 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 90013029 bp After Masking: 79100177 bp Masked: 12.12 % -- Input Database Coverage: 131254290 bp out of 384126663 bp ( 34.17 % ) Sampling Time: 00:11:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2632365 Comparison Time: 03:36:51 (hh:mm:ss) Elapsed Time, 158418 HSPs Collected Number of families returned by RECON: 15008 Round Time: 03:55:18 (hh:mm:ss) Elapsed Time : 173 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 81166 repeats masked totaling 24041588 bp(s). - TE Masking time 00:05:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 252872097 bp Num Contigs Represented = 116 Non ambiguous bp: Initial: 250398053 bp After Masking: 215420807 bp Masked: 13.97 % -- Input Database Coverage: 384126387 bp out of 384126663 bp ( 100.00 % ) Sampling Time: 00:32:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 20266161 Comparison Time: 23:21:48 (hh:mm:ss) Elapsed Time, 586413 HSPs Collected Number of families returned by RECON: 62422 Round Time: 24:57:24 (hh:mm:ss) Elapsed Time : 463 families discovered. RepeatScout/RECON discovery complete: 832 families found Classification Time: 01:49:09 (hh:mm:ss) Elapsed Time Program Time: 31:45:16 (hh:mm:ss) Elapsed Time