RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.5eRazL/RM_1367180.SatFeb151805482025 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: 1739671544 Database = /data/tmp/rModeler.5eRazL/GCA_905231925.1_Smic_04-503SCI.03 - Sequences = 57558 - Bases = 775008844 - N50 = 49981 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1010946-1083086 | [ 1 ] 938807-1010946 | [ ] 866668-938807 | [ 1 ] 794529-866668 | [ 1 ] 722390-794529 | [ 2 ] 650251-722390 | [ ] 578112-650251 | [ 1 ] 505973-578112 | [ ] 433834-505973 | [ 1 ] 361695-433834 | [ 6 ] 289556-361695 | [ 9 ] 217417-289556 | [ 71 ] 145278-217417 | [ 333 ] 73139-145278 |* [ 1872 ] 1000-73139 |************************************************** [ 55260 ] Storage Throughput = excellent ( 1662.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40619316 bp ( 40007093 non ambiguous ) - Num Contigs Represented = 3485 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:59 (hh:mm:ss) Elapsed Time Round Time: 00:11:44 (hh:mm:ss) Elapsed Time : 124 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9335 repeats masked totaling 892801 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10176333 bp Num Contigs Represented = 781 Non ambiguous bp: Initial: 10033228 bp After Masking: 8421988 bp Masked: 16.06 % -- Input Database Coverage: 10176333 bp out of 775008844 bp ( 1.31 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 308505 Comparison Time: 00:06:47 (hh:mm:ss) Elapsed Time, 26767 HSPs Collected Number of families returned by RECON: 1665 Round Time: 00:09:03 (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 : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33302 repeats masked totaling 3528718 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30486062 bp Num Contigs Represented = 2723 Non ambiguous bp: Initial: 30015719 bp After Masking: 24543337 bp Masked: 18.23 % -- Input Database Coverage: 40662395 bp out of 775008844 bp ( 5.25 % ) Sampling Time: 00:01:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3760653 Comparison Time: 00:26:54 (hh:mm:ss) Elapsed Time, 27050 HSPs Collected Number of families returned by RECON: 5066 Round Time: 00:29:14 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108142 repeats masked totaling 11419595 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91314270 bp Num Contigs Represented = 7461 Non ambiguous bp: Initial: 90001927 bp After Masking: 72720198 bp Masked: 19.20 % -- Input Database Coverage: 131976665 bp out of 775008844 bp ( 17.03 % ) Sampling Time: 00:03:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 29333970 Comparison Time: 02:17:38 (hh:mm:ss) Elapsed Time, 216937 HSPs Collected Number of families returned by RECON: 23071 Round Time: 02:27:37 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 349156 repeats masked totaling 38105578 bp(s). - TE Masking time 00:03:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273970837 bp Num Contigs Represented = 22342 Non ambiguous bp: Initial: 270000650 bp After Masking: 214536007 bp Masked: 20.54 % -- Input Database Coverage: 405947502 bp out of 775008844 bp ( 52.38 % ) Sampling Time: 00:13:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284184720 Comparison Time: 15:13:25 (hh:mm:ss) Elapsed Time, 863447 HSPs Collected Number of families returned by RECON: 91572 Round Time: 16:36:08 (hh:mm:ss) Elapsed Time : 690 families discovered. RepeatScout/RECON discovery complete: 1032 families found Classification Time: 00:31:29 (hh:mm:ss) Elapsed Time Program Time: 20:25:15 (hh:mm:ss) Elapsed Time