RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.i3ECBX/RM_3479.ThuJul252322422024 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: 1721974955 Database = /dev/shm/rModeler.i3ECBX/GCF_019740435.1_SWU_Gaff_1.0 - Sequences = 37 - Bases = 680166006 Storage Throughput = excellent ( 1065.73 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41276028 bp ( 40039184 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:37 (hh:mm:ss) Elapsed Time Round Time: 00:39:17 (hh:mm:ss) Elapsed Time : 342 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7607 repeats masked totaling 1058904 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10441507 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10011086 bp After Masking: 8795119 bp Masked: 12.15 % -- Input Database Coverage: 10441507 bp out of 680166006 bp ( 1.54 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 01:17:44 (hh:mm:ss) Elapsed Time, 10059 HSPs Collected Number of families returned by RECON: 1608 Round Time: 01:23:14 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27292 repeats masked totaling 3904048 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30834517 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30028094 bp After Masking: 25609681 bp Masked: 14.71 % -- Input Database Coverage: 41276024 bp out of 680166006 bp ( 6.07 % ) Sampling Time: 00:02:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296835 Comparison Time: 04:01:42 (hh:mm:ss) Elapsed Time, 51125 HSPs Collected Number of families returned by RECON: 5061 Round Time: 04:12:52 (hh:mm:ss) Elapsed Time : 118 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 99578 repeats masked totaling 15044420 bp(s). - TE Masking time 00:01:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92178746 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90030552 bp After Masking: 73507199 bp Masked: 18.35 % -- Input Database Coverage: 133454770 bp out of 680166006 bp ( 19.62 % ) Sampling Time: 00:07:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2659971 Comparison Time: 13:33:27 (hh:mm:ss) Elapsed Time, 223350 HSPs Collected Number of families returned by RECON: 16426 Round Time: 14:07:02 (hh:mm:ss) Elapsed Time : 382 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 359880 repeats masked totaling 57154008 bp(s). - TE Masking time 00:10:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 277408405 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 270008916 bp After Masking: 208737468 bp Masked: 22.69 % -- Input Database Coverage: 410863175 bp out of 680166006 bp ( 60.41 % ) Sampling Time: 00:27:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24092211 Comparison Time: 40:03:59 (hh:mm:ss) Elapsed Time, 735004 HSPs Collected Number of families returned by RECON: 63385 Round Time: 42:18:58 (hh:mm:ss) Elapsed Time : 968 families discovered. RepeatScout/RECON discovery complete: 1831 families found Classification Time: 01:43:52 (hh:mm:ss) Elapsed Time Program Time: 64:25:15 (hh:mm:ss) Elapsed Time