RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.W8CuSy/RM_25550.WedDec40612442024 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: 1733321562 Database = /scratch/tmp/rModeler.W8CuSy/GCA_029281585.3_NHGRI_mGorGor1-v2.1_pri - Sequences = 26 - Bases = 3545850631 Storage Throughput = fair ( 633.28 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001784 bp ( 40001784 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:28:00 (hh:mm:ss) Elapsed Time Round Time: 00:42:59 (hh:mm:ss) Elapsed Time : 217 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10778 repeats masked totaling 2520925 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000447 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000447 bp After Masking: 5622009 bp Masked: 43.78 % -- Input Database Coverage: 10000447 bp out of 3545850631 bp ( 0.28 % ) Sampling Time: 00:10:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:42 (hh:mm:ss) Elapsed Time, 3868 HSPs Collected Number of families returned by RECON: 713 Round Time: 00:15:22 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34451 repeats masked totaling 8070508 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001332 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30001332 bp After Masking: 16305716 bp Masked: 45.65 % -- Input Database Coverage: 40001779 bp out of 3545850631 bp ( 1.13 % ) Sampling Time: 00:24:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:24:09 (hh:mm:ss) Elapsed Time, 30514 HSPs Collected Number of families returned by RECON: 2323 Round Time: 00:55:30 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:04:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 117614 repeats masked totaling 27773474 bp(s). - TE Masking time 00:01:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044817 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90004810 bp After Masking: 46825621 bp Masked: 47.97 % -- Input Database Coverage: 130046596 bp out of 3545850631 bp ( 3.67 % ) Sampling Time: 01:09:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 02:31:39 (hh:mm:ss) Elapsed Time, 97368 HSPs Collected Number of families returned by RECON: 6622 Round Time: 03:45:59 (hh:mm:ss) Elapsed Time : 195 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:53:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 379192 repeats masked totaling 90402831 bp(s). - TE Masking time 00:06:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270215034 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270037654 bp After Masking: 132603553 bp Masked: 50.89 % -- Input Database Coverage: 400261630 bp out of 3545850631 bp ( 11.29 % ) Sampling Time: 03:11:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 18:59:34 (hh:mm:ss) Elapsed Time, 227023 HSPs Collected Number of families returned by RECON: 24634 Round Time: 22:37:57 (hh:mm:ss) Elapsed Time : 338 families discovered. RepeatScout/RECON discovery complete: 833 families found Classification Time: 00:41:41 (hh:mm:ss) Elapsed Time Program Time: 28:59:29 (hh:mm:ss) Elapsed Time