RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nD0BGf/RM_93990.ThuMar211520592024 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: 1711059658 Database = /dev/shm/rModeler.nD0BGf/GCA_036417475.1_mIniGeo1.hap2 - Sequences = 800 - Bases = 2540437634 - N50 = 116813625 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 175238054-187754987 | [ 3 ] 162721122-175238054 | [ 1 ] 150204189-162721121 | [ 1 ] 137687257-150204189 | [ ] 125170324-137687256 | [ 1 ] 112653392-125170324 | [ 2 ] 100136459-112653391 | [ 4 ] 87619527-100136459 | [ 4 ] 75102594-87619526 | [ 2 ] 62585662-75102594 | [ 2 ] 50068729-62585661 | [ ] 37551797-50068729 | [ ] 25034864-37551796 | [ 1 ] 12517932-25034864 | [ ] 1000-12517932 |************************************************** [ 779 ] Storage Throughput = good ( 776.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022352 bp ( 40021952 non ambiguous ) - Num Contigs Represented = 94 - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:29 (hh:mm:ss) Elapsed Time Round Time: 00:32:02 (hh:mm:ss) Elapsed Time : 199 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9774 repeats masked totaling 3107954 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008769 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10008369 bp After Masking: 6537965 bp Masked: 34.68 % -- Input Database Coverage: 10008769 bp out of 2540437634 bp ( 0.39 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 7815 HSPs Collected Number of families returned by RECON: 724 Round Time: 00:07:07 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:47 (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... 33598 repeats masked totaling 10339232 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013581 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 30013581 bp After Masking: 18657001 bp Masked: 37.84 % -- Input Database Coverage: 40022350 bp out of 2540437634 bp ( 1.58 % ) Sampling Time: 00:03:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:24:39 (hh:mm:ss) Elapsed Time, 34024 HSPs Collected Number of families returned by RECON: 2327 Round Time: 00:29:12 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 110170 repeats masked totaling 33365242 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040740 bp Num Contigs Represented = 137 Non ambiguous bp: Initial: 90038940 bp After Masking: 54360160 bp Masked: 39.63 % -- Input Database Coverage: 130063090 bp out of 2540437634 bp ( 5.12 % ) Sampling Time: 00:10:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 02:33:21 (hh:mm:ss) Elapsed Time, 158207 HSPs Collected Number of families returned by RECON: 7709 Round Time: 02:46:56 (hh:mm:ss) Elapsed Time : 150 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 362583 repeats masked totaling 107746815 bp(s). - TE Masking time 00:04:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270013535 bp Num Contigs Represented = 301 Non ambiguous bp: Initial: 270008735 bp After Masking: 153286934 bp Masked: 43.23 % -- Input Database Coverage: 400076625 bp out of 2540437634 bp ( 15.75 % ) Sampling Time: 00:33:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23116600 Comparison Time: 17:44:19 (hh:mm:ss) Elapsed Time, 498442 HSPs Collected Number of families returned by RECON: 30876 Round Time: 18:39:07 (hh:mm:ss) Elapsed Time : 344 families discovered. RepeatScout/RECON discovery complete: 762 families found Classification Time: 00:28:37 (hh:mm:ss) Elapsed Time Program Time: 23:03:01 (hh:mm:ss) Elapsed Time