RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.RXlRRi/RM_3454336.FriApr181510162025 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: 1745014216 Database = /data/tmp/rModeler.RXlRRi/GCA_048128715.1_fSymNem1.1_haplotype_2 - Sequences = 60 - Bases = 1079709985 Storage Throughput = good ( 846.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040476 bp ( 40039776 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:13 (hh:mm:ss) Elapsed Time Round Time: 00:32:20 (hh:mm:ss) Elapsed Time : 1057 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21037 repeats masked totaling 2765277 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000995 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000795 bp After Masking: 7010823 bp Masked: 29.90 % -- Input Database Coverage: 10000995 bp out of 1079709985 bp ( 0.93 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:22 (hh:mm:ss) Elapsed Time, 15071 HSPs Collected Number of families returned by RECON: 2099 Round Time: 00:09:24 (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 : 00:00:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66233 repeats masked totaling 8903327 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039463 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30038963 bp After Masking: 20512397 bp Masked: 31.71 % -- Input Database Coverage: 40040458 bp out of 1079709985 bp ( 3.71 % ) Sampling Time: 00:04:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:31:29 (hh:mm:ss) Elapsed Time, 111742 HSPs Collected Number of families returned by RECON: 6539 Round Time: 00:49:04 (hh:mm:ss) Elapsed Time : 286 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 219394 repeats masked totaling 30288345 bp(s). - TE Masking time 00:04:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90033725 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90032825 bp After Masking: 57693381 bp Masked: 35.92 % -- Input Database Coverage: 130074183 bp out of 1079709985 bp ( 12.05 % ) Sampling Time: 00:14:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 03:19:10 (hh:mm:ss) Elapsed Time, 381527 HSPs Collected Number of families returned by RECON: 18128 Round Time: 04:17:02 (hh:mm:ss) Elapsed Time : 713 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 746710 repeats masked totaling 110701155 bp(s). - TE Masking time 00:17:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031735 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 270028135 bp After Masking: 153158454 bp Masked: 43.28 % -- Input Database Coverage: 400105918 bp out of 1079709985 bp ( 37.06 % ) Sampling Time: 00:42:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22825146 Comparison Time: 20:20:03 (hh:mm:ss) Elapsed Time, 847777 HSPs Collected Number of families returned by RECON: 55247 Round Time: 24:45:24 (hh:mm:ss) Elapsed Time : 1493 families discovered. RepeatScout/RECON discovery complete: 3574 families found Classification Time: 01:48:36 (hh:mm:ss) Elapsed Time Program Time: 32:21:50 (hh:mm:ss) Elapsed Time