RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.dx7cre/RM_3881642.SatNov160223342024 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: 1731752614 Database = /scratch/tmp/rModeler.dx7cre/GCF_028021215.1_mEscRob2.pri - Sequences = 703 - Bases = 2982418581 - N50 = 130624547 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 187550578-200946153 | [ 2 ] 174155003-187550577 | [ 1 ] 160759429-174155003 | [ ] 147363854-160759428 | [ 2 ] 133968280-147363854 | [ 3 ] 120572705-133968279 | [ 2 ] 107177131-120572705 | [ 3 ] 93781556-107177130 | [ 3 ] 80385982-93781556 | [ 3 ] 66990407-80385981 | [ 2 ] 53594833-66990407 | [ ] 40199258-53594832 | [ 1 ] 26803684-40199258 | [ ] 13408109-26803683 | [ ] 12535-13408109 |************************************************** [ 681 ] Storage Throughput = excellent ( 1449.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028732 bp ( 40028532 non ambiguous ) - Num Contigs Represented = 118 - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:52 (hh:mm:ss) Elapsed Time Round Time: 00:15:31 (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 : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9487 repeats masked totaling 3045626 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020471 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10020471 bp After Masking: 6611855 bp Masked: 34.02 % -- Input Database Coverage: 10020471 bp out of 2982418581 bp ( 0.34 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:11 (hh:mm:ss) Elapsed Time, 94962 HSPs Collected Number of families returned by RECON: 842 Round Time: 00:05:38 (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 : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33198 repeats masked totaling 11169974 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008256 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 30008056 bp After Masking: 17972369 bp Masked: 40.11 % -- Input Database Coverage: 40028727 bp out of 2982418581 bp ( 1.34 % ) Sampling Time: 00:01:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:12:24 (hh:mm:ss) Elapsed Time, 103130 HSPs Collected Number of families returned by RECON: 2138 Round Time: 00:21:41 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 105776 repeats masked totaling 34607721 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010320 bp Num Contigs Represented = 189 Non ambiguous bp: Initial: 90008469 bp After Masking: 50920116 bp Masked: 43.43 % -- Input Database Coverage: 130039047 bp out of 2982418581 bp ( 4.36 % ) Sampling Time: 00:06:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 01:05:29 (hh:mm:ss) Elapsed Time, 538612 HSPs Collected Number of families returned by RECON: 7384 Round Time: 01:14:03 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 361293 repeats masked totaling 112823875 bp(s). - TE Masking time 00:01:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019674 bp Num Contigs Represented = 363 Non ambiguous bp: Initial: 270015474 bp After Masking: 145087672 bp Masked: 46.27 % -- Input Database Coverage: 400058721 bp out of 2982418581 bp ( 13.41 % ) Sampling Time: 00:18:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 07:37:48 (hh:mm:ss) Elapsed Time, 5909606 HSPs Collected Number of families returned by RECON: 27739 Round Time: 08:09:03 (hh:mm:ss) Elapsed Time : 343 families discovered. RepeatScout/RECON discovery complete: 793 families found Classification Time: 00:17:35 (hh:mm:ss) Elapsed Time Program Time: 10:23:31 (hh:mm:ss) Elapsed Time