RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ak0SJr/RM_1638669.WedFeb260843542025 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: 1740588233 Database = /dev/shm/rModeler.ak0SJr/GCF_039877785.1_fChaTrf1.hap1 - Sequences = 36 - Bases = 662489023 Storage Throughput = excellent ( 1889.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039157 bp ( 40038357 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:18 (hh:mm:ss) Elapsed Time Round Time: 00:09:40 (hh:mm:ss) Elapsed Time : 358 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6185 repeats masked totaling 990705 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002583 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10002183 bp After Masking: 8689442 bp Masked: 13.12 % -- Input Database Coverage: 10002583 bp out of 662489023 bp ( 1.51 % ) Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:55 (hh:mm:ss) Elapsed Time, 8072 HSPs Collected Number of families returned by RECON: 1550 Round Time: 00:03:24 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20077 repeats masked totaling 3003301 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036494 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30036094 bp After Masking: 26027141 bp Masked: 13.35 % -- Input Database Coverage: 40039077 bp out of 662489023 bp ( 6.04 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:14:02 (hh:mm:ss) Elapsed Time, 44710 HSPs Collected Number of families returned by RECON: 5752 Round Time: 00:15:45 (hh:mm:ss) Elapsed Time : 109 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71892 repeats masked totaling 11378504 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027636 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90026436 bp After Masking: 75562023 bp Masked: 16.07 % -- Input Database Coverage: 130066713 bp out of 662489023 bp ( 19.63 % ) Sampling Time: 00:03:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:21:25 (hh:mm:ss) Elapsed Time, 252952 HSPs Collected Number of families returned by RECON: 20801 Round Time: 01:30:04 (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 : 00:01:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 277074 repeats masked totaling 47053684 bp(s). - TE Masking time 00:02:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270029427 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 270024227 bp After Masking: 215648230 bp Masked: 20.14 % -- Input Database Coverage: 400096140 bp out of 662489023 bp ( 60.39 % ) Sampling Time: 00:10:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 09:40:22 (hh:mm:ss) Elapsed Time, 827892 HSPs Collected Number of families returned by RECON: 83006 Round Time: 10:43:54 (hh:mm:ss) Elapsed Time : 1107 families discovered. RepeatScout/RECON discovery complete: 2044 families found Classification Time: 00:46:23 (hh:mm:ss) Elapsed Time Program Time: 13:29:10 (hh:mm:ss) Elapsed Time