RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.CGKaqx/RM_8345.FriJul51243232024 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: 1720208602 Database = /dev/shm/rModeler.CGKaqx/GCF_000732505.1_C_variegatus-1.0 - Sequences = 9259 - Bases = 1035184475 - N50 = 835642 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 4215007-4516015 | [ 1 ] 3913999-4215006 | [ ] 3612991-3913998 | [ 1 ] 3311983-3612990 | [ 2 ] 3010975-3311982 | [ 4 ] 2709967-3010974 | [ 7 ] 2408959-2709966 | [ 13 ] 2107952-2408959 | [ 15 ] 1806944-2107951 | [ 27 ] 1505936-1806943 | [ 42 ] 1204928-1505935 | [ 82 ] 903920-1204927 | [ 129 ] 602912-903919 |* [ 221 ] 301904-602911 |** [ 437 ] 897-301904 |************************************************** [ 8278 ] Storage Throughput = excellent ( 1041.15 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 46181135 bp ( 40005505 non ambiguous ) - Num Contigs Represented = 1097 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:35 (hh:mm:ss) Elapsed Time Round Time: 00:24:38 (hh:mm:ss) Elapsed Time : 764 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 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13449 repeats masked totaling 2275163 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11590096 bp Num Contigs Represented = 322 Non ambiguous bp: Initial: 10034533 bp After Masking: 7665086 bp Masked: 23.61 % -- Input Database Coverage: 11590096 bp out of 1035184475 bp ( 1.12 % ) Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 63903 Comparison Time: 00:07:31 (hh:mm:ss) Elapsed Time, 7960 HSPs Collected Number of families returned by RECON: 1475 Round Time: 00:08:29 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41442 repeats masked totaling 7013212 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 34630906 bp Num Contigs Represented = 901 Non ambiguous bp: Initial: 30004097 bp After Masking: 22709108 bp Masked: 24.31 % -- Input Database Coverage: 46221002 bp out of 1035184475 bp ( 4.47 % ) Sampling Time: 00:01:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 652653 Comparison Time: 00:41:15 (hh:mm:ss) Elapsed Time, 44892 HSPs Collected Number of families returned by RECON: 4561 Round Time: 00:44:36 (hh:mm:ss) Elapsed Time : 129 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 137549 repeats masked totaling 23674266 bp(s). - TE Masking time 00:02:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 103673661 bp Num Contigs Represented = 1925 Non ambiguous bp: Initial: 90013770 bp After Masking: 65530391 bp Masked: 27.20 % -- Input Database Coverage: 149894663 bp out of 1035184475 bp ( 14.48 % ) Sampling Time: 00:05:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 5599531 Comparison Time: 04:50:22 (hh:mm:ss) Elapsed Time, 234884 HSPs Collected Number of families returned by RECON: 14572 Round Time: 05:07:59 (hh:mm:ss) Elapsed Time : 505 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 489673 repeats masked totaling 84385185 bp(s). - TE Masking time 00:13:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 309939540 bp Num Contigs Represented = 4025 Non ambiguous bp: Initial: 270022147 bp After Masking: 183291616 bp Masked: 32.12 % -- Input Database Coverage: 459834203 bp out of 1035184475 bp ( 44.42 % ) Sampling Time: 00:22:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 50135091 Comparison Time: 37:20:36 (hh:mm:ss) Elapsed Time, 586794 HSPs Collected Number of families returned by RECON: 48530 Round Time: 39:03:59 (hh:mm:ss) Elapsed Time : 1173 families discovered. RepeatScout/RECON discovery complete: 2592 families found Classification Time: 01:34:30 (hh:mm:ss) Elapsed Time Program Time: 47:04:11 (hh:mm:ss) Elapsed Time