RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9B06WN/RM_135846.FriJul182302502025 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: 1752904970 Database = /dev/shm/rModeler.9B06WN/GCA_048301605.1_SynTyp1_v1.hap2 - Sequences = 125 - Bases = 356339685 - N50 = 15395927 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 26938847-28862979 | [ 2 ] 25014715-26938846 | [ ] 23090583-25014714 | [ ] 21166451-23090582 | [ 1 ] 19242319-21166450 | [ 1 ] 17318187-19242318 |* [ 3 ] 15394055-17318186 | [ 1 ] 13469923-15394054 |* [ 4 ] 11545791-13469922 |* [ 3 ] 9621659-11545790 | [ 2 ] 7697527-9621658 |* [ 3 ] 5773395-7697526 | [ 2 ] 3849263-5773394 | [ ] 1925131-3849262 | [ ] 1000-1925131 |************************************************** [ 103 ] Storage Throughput = excellent ( 1681.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014119 bp ( 40013019 non ambiguous ) - Num Contigs Represented = 69 - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:44 (hh:mm:ss) Elapsed Time Round Time: 00:09:46 (hh:mm:ss) Elapsed Time : 323 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5472 repeats masked totaling 1498094 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006578 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10006478 bp After Masking: 7779725 bp Masked: 22.25 % -- Input Database Coverage: 10006578 bp out of 356339685 bp ( 2.81 % ) Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:46 (hh:mm:ss) Elapsed Time, 8627 HSPs Collected Number of families returned by RECON: 1053 Round Time: 00:03:21 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18169 repeats masked totaling 5008406 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007461 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 30006461 bp After Masking: 21730167 bp Masked: 27.58 % -- Input Database Coverage: 40014039 bp out of 356339685 bp ( 11.23 % ) Sampling Time: 00:01:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:11:59 (hh:mm:ss) Elapsed Time, 24835 HSPs Collected Number of families returned by RECON: 3707 Round Time: 00:14:33 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59364 repeats masked totaling 15822036 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040677 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 90038977 bp After Masking: 65815778 bp Masked: 26.90 % -- Input Database Coverage: 130054716 bp out of 356339685 bp ( 36.50 % ) Sampling Time: 00:05:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 01:10:42 (hh:mm:ss) Elapsed Time, 397381 HSPs Collected Number of families returned by RECON: 15696 Round Time: 01:20:13 (hh:mm:ss) Elapsed Time : 313 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 188794 repeats masked totaling 47219496 bp(s). - TE Masking time 00:02:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 226284712 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 226278512 bp After Masking: 157807246 bp Masked: 30.26 % -- Input Database Coverage: 356339428 bp out of 356339685 bp ( 100.00 % ) Sampling Time: 00:13:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 16236451 Comparison Time: 06:02:18 (hh:mm:ss) Elapsed Time, 546077 HSPs Collected Number of families returned by RECON: 47580 Round Time: 06:33:29 (hh:mm:ss) Elapsed Time : 630 families discovered. RepeatScout/RECON discovery complete: 1331 families found Classification Time: 00:33:53 (hh:mm:ss) Elapsed Time Program Time: 08:55:15 (hh:mm:ss) Elapsed Time