RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6BQtAC/RM_3232837.WedApr160549582025 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: 1744807797 Database = /dev/shm/rModeler.6BQtAC/GCA_965152285.1_rEreImb1.hap2 - Sequences = 41 - Bases = 2224324466 Storage Throughput = excellent ( 1771.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40082694 bp ( 40002694 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:56 (hh:mm:ss) Elapsed Time Round Time: 00:11:58 (hh:mm:ss) Elapsed Time : 535 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 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13419 repeats masked totaling 2887334 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000487 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10000487 bp After Masking: 7028131 bp Masked: 29.72 % -- Input Database Coverage: 10000487 bp out of 2224324466 bp ( 0.45 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:09 (hh:mm:ss) Elapsed Time, 16210 HSPs Collected Number of families returned by RECON: 1742 Round Time: 00:04:08 (hh:mm:ss) Elapsed Time : 33 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45994 repeats masked totaling 9751585 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30082127 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30002127 bp After Masking: 20047648 bp Masked: 33.18 % -- Input Database Coverage: 40082614 bp out of 2224324466 bp ( 1.80 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:13:34 (hh:mm:ss) Elapsed Time, 141336 HSPs Collected Number of families returned by RECON: 5101 Round Time: 00:16:50 (hh:mm:ss) Elapsed Time : 133 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 152044 repeats masked totaling 32250940 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90170076 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90026494 bp After Masking: 57145246 bp Masked: 36.52 % -- Input Database Coverage: 130252690 bp out of 2224324466 bp ( 5.86 % ) Sampling Time: 00:05:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:23:24 (hh:mm:ss) Elapsed Time, 1074408 HSPs Collected Number of families returned by RECON: 14779 Round Time: 01:37:28 (hh:mm:ss) Elapsed Time : 455 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 524141 repeats masked totaling 111477454 bp(s). - TE Masking time 00:03:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270394294 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 270019789 bp After Masking: 156307636 bp Masked: 42.11 % -- Input Database Coverage: 400646984 bp out of 2224324466 bp ( 18.01 % ) Sampling Time: 00:20:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 08:31:02 (hh:mm:ss) Elapsed Time, 7559587 HSPs Collected Number of families returned by RECON: 42765 Round Time: 09:17:14 (hh:mm:ss) Elapsed Time : 1057 families discovered. RepeatScout/RECON discovery complete: 2213 families found Classification Time: 00:42:44 (hh:mm:ss) Elapsed Time Program Time: 12:10:22 (hh:mm:ss) Elapsed Time