RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.TQD05U/RM_3515490.ThuApr101845282025 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: 1744335926 Database = /dev/shm/rModeler.TQD05U/GCF_037993035.1_T2T-MFA8v1.0 - Sequences = 21 - Bases = 3042914375 Storage Throughput = excellent ( 1818.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001674 bp ( 40001674 non ambiguous ) - Num Contigs Represented = 21 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:15 (hh:mm:ss) Elapsed Time Round Time: 00:11:48 (hh:mm:ss) Elapsed Time : 249 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12097 repeats masked totaling 2609631 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000394 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10000394 bp After Masking: 6423271 bp Masked: 35.77 % -- Input Database Coverage: 10000394 bp out of 3042914375 bp ( 0.33 % ) Sampling Time: 00:00:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:48 (hh:mm:ss) Elapsed Time, 6933 HSPs Collected Number of families returned by RECON: 883 Round Time: 00:03:30 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44985 repeats masked totaling 9332838 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001276 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 30001276 bp After Masking: 18470333 bp Masked: 38.43 % -- Input Database Coverage: 40001670 bp out of 3042914375 bp ( 1.31 % ) Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:12:05 (hh:mm:ss) Elapsed Time, 27763 HSPs Collected Number of families returned by RECON: 2305 Round Time: 00:13:57 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 142551 repeats masked totaling 30500396 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003831 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 90003831 bp After Masking: 53282720 bp Masked: 40.80 % -- Input Database Coverage: 130005501 bp out of 3042914375 bp ( 4.27 % ) Sampling Time: 00:04:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 01:06:56 (hh:mm:ss) Elapsed Time, 120834 HSPs Collected Number of families returned by RECON: 8254 Round Time: 01:13:00 (hh:mm:ss) Elapsed Time : 188 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 451407 repeats masked totaling 97096996 bp(s). - TE Masking time 00:02:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270011561 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 270011561 bp After Masking: 152575051 bp Masked: 43.49 % -- Input Database Coverage: 400017062 bp out of 3042914375 bp ( 13.15 % ) Sampling Time: 00:14:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22777875 Comparison Time: 07:25:00 (hh:mm:ss) Elapsed Time, 1052580 HSPs Collected Number of families returned by RECON: 32312 Round Time: 07:53:04 (hh:mm:ss) Elapsed Time : 415 families discovered. RepeatScout/RECON discovery complete: 939 families found Classification Time: 00:19:14 (hh:mm:ss) Elapsed Time Program Time: 09:54:33 (hh:mm:ss) Elapsed Time