RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.THchlV/RM_2379047.ThuFeb270133532025 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: 1740648832 Database = /data/tmp/rModeler.THchlV/GCA_047948215.1_ASM4794821v1 - Sequences = 13 - Bases = 2201051051 Storage Throughput = excellent ( 1577.24 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000575 bp ( 40000375 non ambiguous ) - Num Contigs Represented = 13 - Sequence extraction : 00:02:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:44 (hh:mm:ss) Elapsed Time Round Time: 00:18:47 (hh:mm:ss) Elapsed Time : 769 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 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13653 repeats masked totaling 3379126 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000110 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 10000110 bp After Masking: 6508463 bp Masked: 34.92 % -- Input Database Coverage: 10000110 bp out of 2201051051 bp ( 0.45 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:15 (hh:mm:ss) Elapsed Time, 7661 HSPs Collected Number of families returned by RECON: 1318 Round Time: 00:06:43 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41170 repeats masked totaling 10294757 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000464 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 30000264 bp After Masking: 19376005 bp Masked: 35.41 % -- Input Database Coverage: 40000574 bp out of 2201051051 bp ( 1.82 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:29:54 (hh:mm:ss) Elapsed Time, 50589 HSPs Collected Number of families returned by RECON: 4477 Round Time: 00:34:53 (hh:mm:ss) Elapsed Time : 103 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 136262 repeats masked totaling 34446485 bp(s). - TE Masking time 00:02:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90001275 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 90000275 bp After Masking: 54424814 bp Masked: 39.53 % -- Input Database Coverage: 130001849 bp out of 2201051051 bp ( 5.91 % ) Sampling Time: 00:11:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 03:07:31 (hh:mm:ss) Elapsed Time, 281662 HSPs Collected Number of families returned by RECON: 12073 Round Time: 03:25:06 (hh:mm:ss) Elapsed Time : 479 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 477783 repeats masked totaling 121142553 bp(s). - TE Masking time 00:13:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270008648 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 270006748 bp After Masking: 145646336 bp Masked: 46.06 % -- Input Database Coverage: 400010497 bp out of 2201051051 bp ( 18.17 % ) Sampling Time: 00:40:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 21:15:31 (hh:mm:ss) Elapsed Time, 845121 HSPs Collected Number of families returned by RECON: 30004 Round Time: 22:17:22 (hh:mm:ss) Elapsed Time : 1080 families discovered. RepeatScout/RECON discovery complete: 2445 families found Classification Time: 01:24:56 (hh:mm:ss) Elapsed Time Program Time: 28:07:47 (hh:mm:ss) Elapsed Time