RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9CYB1M/RM_2766943.FriJul181029212025 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: 1752859760 Database = /dev/shm/rModeler.9CYB1M/GCA_047774235.1_bZonAlb1.hap2 - Sequences = 150 - Bases = 1176404578 - N50 = 74313678 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 146382412-156836853 | [ 1 ] 135927972-146382412 | [ ] 125473532-135927972 | [ ] 115019092-125473532 | [ 2 ] 104564652-115019092 | [ ] 94110212-104564652 | [ ] 83655772-94110212 | [ ] 73201331-83655771 | [ 2 ] 62746891-73201331 | [ 1 ] 52292451-62746891 | [ 1 ] 41838011-52292451 | [ 1 ] 31383571-41838011 | [ 2 ] 20929131-31383571 |* [ 4 ] 10474691-20929131 |*** [ 10 ] 20251-10474691 |************************************************** [ 126 ] Storage Throughput = excellent ( 1134.98 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028941 bp ( 40027641 non ambiguous ) - Num Contigs Represented = 70 - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:04 (hh:mm:ss) Elapsed Time Round Time: 00:51:04 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3033 repeats masked totaling 1365509 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038163 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10037563 bp After Masking: 8036838 bp Masked: 19.93 % -- Input Database Coverage: 10038163 bp out of 1176404578 bp ( 0.85 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:14 (hh:mm:ss) Elapsed Time, 936 HSPs Collected Number of families returned by RECON: 294 Round Time: 00:06:48 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10272 repeats masked totaling 3883435 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030777 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30030077 bp After Masking: 23820161 bp Masked: 20.68 % -- Input Database Coverage: 40068940 bp out of 1176404578 bp ( 3.41 % ) Sampling Time: 00:05:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:31:01 (hh:mm:ss) Elapsed Time, 8951 HSPs Collected Number of families returned by RECON: 1800 Round Time: 00:37:37 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33190 repeats masked totaling 12471330 bp(s). - TE Masking time 00:02:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90014927 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 90012127 bp After Masking: 70754565 bp Masked: 21.39 % -- Input Database Coverage: 130083867 bp out of 1176404578 bp ( 11.06 % ) Sampling Time: 00:14:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:53:29 (hh:mm:ss) Elapsed Time, 94750 HSPs Collected Number of families returned by RECON: 10256 Round Time: 04:18:13 (hh:mm:ss) Elapsed Time : 132 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111097 repeats masked totaling 42780467 bp(s). - TE Masking time 00:09:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036754 bp Num Contigs Represented = 107 Non ambiguous bp: Initial: 270026754 bp After Masking: 207069331 bp Masked: 23.32 % -- Input Database Coverage: 400120621 bp out of 1176404578 bp ( 34.01 % ) Sampling Time: 00:45:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 31:37:02 (hh:mm:ss) Elapsed Time, 298462 HSPs Collected Number of families returned by RECON: 63484 Round Time: 33:33:17 (hh:mm:ss) Elapsed Time : 332 families discovered. RepeatScout/RECON discovery complete: 683 families found Classification Time: 01:06:09 (hh:mm:ss) Elapsed Time Program Time: 40:33:08 (hh:mm:ss) Elapsed Time