RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QaUEfA/RM_11070.TueNov280734112023 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: 1701185650 Database = /dev/shm/rModeler.QaUEfA/GCA_028021215.1_mEscRob2.pri - Sequences = 704 - Bases = 2982434994 - 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 |************************************************** [ 682 ] Storage Throughput = excellent ( 1218.37 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033324 bp ( 40031724 non ambiguous ) - Num Contigs Represented = 122 - Sequence extraction : 00:02:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:27:50 (hh:mm:ss) Elapsed Time Round Time: 00:46:04 (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 : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9716 repeats masked totaling 3210541 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011718 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10011518 bp After Masking: 6490812 bp Masked: 35.17 % -- Input Database Coverage: 10011718 bp out of 2982434994 bp ( 0.34 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:07:51 (hh:mm:ss) Elapsed Time, 569660 HSPs Collected Number of families returned by RECON: 703 Round Time: 00:26:31 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34233 repeats masked totaling 11771819 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021526 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 30020126 bp After Masking: 16650833 bp Masked: 44.53 % -- Input Database Coverage: 40033244 bp out of 2982434994 bp ( 1.34 % ) Sampling Time: 00:04:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:25:01 (hh:mm:ss) Elapsed Time, 26709 HSPs Collected Number of families returned by RECON: 1926 Round Time: 00:30:27 (hh:mm:ss) Elapsed Time : 47 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 110344 repeats masked totaling 35547129 bp(s). - TE Masking time 00:01:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035406 bp Num Contigs Represented = 184 Non ambiguous bp: Initial: 90034206 bp After Masking: 50407073 bp Masked: 44.01 % -- Input Database Coverage: 130068650 bp out of 2982434994 bp ( 4.36 % ) Sampling Time: 00:12:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 02:53:28 (hh:mm:ss) Elapsed Time, 108316 HSPs Collected Number of families returned by RECON: 7628 Round Time: 03:11:03 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 376545 repeats masked totaling 117264119 bp(s). - TE Masking time 00:05:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270005422 bp Num Contigs Represented = 349 Non ambiguous bp: Initial: 270003222 bp After Masking: 141910544 bp Masked: 47.44 % -- Input Database Coverage: 400074072 bp out of 2982434994 bp ( 13.41 % ) Sampling Time: 00:38:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 20:02:16 (hh:mm:ss) Elapsed Time, 290584 HSPs Collected Number of families returned by RECON: 28622 Round Time: 21:02:12 (hh:mm:ss) Elapsed Time : 335 families discovered. RepeatScout/RECON discovery complete: 767 families found Classification Time: 00:34:03 (hh:mm:ss) Elapsed Time Program Time: 26:30:20 (hh:mm:ss) Elapsed Time