RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QfDX48/RM_22627.FriDec11540292023 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: 1701474027 Database = /dev/shm/rModeler.QfDX48/GCF_027887165.1_mMonDom1.pri - Sequences = 13 - Bases = 3586166573 Storage Throughput = excellent ( 1769.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40320102 bp ( 40008899 non ambiguous ) - Num Contigs Represented = 9 - Sequence extraction : 00:10:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:27 (hh:mm:ss) Elapsed Time Round Time: 00:31:17 (hh:mm:ss) Elapsed Time : 437 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18826 repeats masked totaling 3889869 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039987 bp Num Contigs Represented = 9 Non ambiguous bp: Initial: 10004412 bp After Masking: 5963230 bp Masked: 40.39 % -- Input Database Coverage: 10039987 bp out of 3586166573 bp ( 0.28 % ) Sampling Time: 00:03:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:19 (hh:mm:ss) Elapsed Time, 10885 HSPs Collected Number of families returned by RECON: 1206 Round Time: 00:11:06 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64356 repeats masked totaling 13539024 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30280035 bp Num Contigs Represented = 9 Non ambiguous bp: Initial: 30004407 bp After Masking: 15959698 bp Masked: 46.81 % -- Input Database Coverage: 40320022 bp out of 3586166573 bp ( 1.12 % ) Sampling Time: 00:09:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:25:00 (hh:mm:ss) Elapsed Time, 33569 HSPs Collected Number of families returned by RECON: 3304 Round Time: 00:35:38 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:17:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 200370 repeats masked totaling 42856366 bp(s). - TE Masking time 00:01:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90880579 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 90022937 bp After Masking: 45705349 bp Masked: 49.23 % -- Input Database Coverage: 131200601 bp out of 3586166573 bp ( 3.66 % ) Sampling Time: 00:22:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 01:50:14 (hh:mm:ss) Elapsed Time, 119229 HSPs Collected Number of families returned by RECON: 9872 Round Time: 02:16:40 (hh:mm:ss) Elapsed Time : 240 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:07:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 669435 repeats masked totaling 139941507 bp(s). - TE Masking time 00:04:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272241629 bp Num Contigs Represented = 10 Non ambiguous bp: Initial: 270031517 bp After Masking: 125847231 bp Masked: 53.40 % -- Input Database Coverage: 403442230 bp out of 3586166573 bp ( 11.25 % ) Sampling Time: 01:24:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23157415 Comparison Time: 13:06:19 (hh:mm:ss) Elapsed Time, 258958 HSPs Collected Number of families returned by RECON: 34453 Round Time: 14:54:26 (hh:mm:ss) Elapsed Time : 531 families discovered. RepeatScout/RECON discovery complete: 1314 families found Classification Time: 00:39:50 (hh:mm:ss) Elapsed Time Program Time: 19:08:57 (hh:mm:ss) Elapsed Time