RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Vca2ax/RM_1244590.WedDec181105132024 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: 1734548712 Database = /dev/shm/rModeler.Vca2ax/GCA_039878515.1_bCotChi1.hap1 - Sequences = 425 - Bases = 974517173 - N50 = 104650380 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 172627408-184957057 | [ 1 ] 160297759-172627407 | [ ] 147968110-160297758 | [ ] 135638461-147968109 | [ 1 ] 123308812-135638460 | [ ] 110979163-123308811 | [ ] 98649514-110979162 | [ 1 ] 86319866-98649514 | [ ] 73990217-86319865 | [ 1 ] 61660568-73990216 | [ 1 ] 49330919-61660567 | [ 1 ] 37001270-49330918 | [ ] 24671621-37001269 | [ 3 ] 12341972-24671620 | [ 7 ] 12324-12341972 |************************************************** [ 409 ] Storage Throughput = fair ( 481.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027685 bp ( 40024785 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:04:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:34:22 (hh:mm:ss) Elapsed Time Round Time: 00:46:56 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3862 repeats masked totaling 895794 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007434 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10006434 bp After Masking: 8939154 bp Masked: 10.67 % -- Input Database Coverage: 10007434 bp out of 974517173 bp ( 1.03 % ) Sampling Time: 00:02:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:15:31 (hh:mm:ss) Elapsed Time, 713 HSPs Collected Number of families returned by RECON: 252 Round Time: 00:17:55 (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 : 00:02:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11329 repeats masked totaling 2956011 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30020171 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 30018271 bp After Masking: 26707200 bp Masked: 11.03 % -- Input Database Coverage: 40027605 bp out of 974517173 bp ( 4.11 % ) Sampling Time: 00:05:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 01:45:08 (hh:mm:ss) Elapsed Time, 4773 HSPs Collected Number of families returned by RECON: 1494 Round Time: 01:51:00 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34114 repeats masked totaling 8135821 bp(s). - TE Masking time 00:03:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031356 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 90024156 bp After Masking: 80241137 bp Masked: 10.87 % -- Input Database Coverage: 130058961 bp out of 974517173 bp ( 13.35 % ) Sampling Time: 00:21:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 15:28:58 (hh:mm:ss) Elapsed Time, 41853 HSPs Collected Number of families returned by RECON: 9714 Round Time: 15:57:37 (hh:mm:ss) Elapsed Time : 47 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109241 repeats masked totaling 26758539 bp(s). - TE Masking time 00:12:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270053155 bp Num Contigs Represented = 195 Non ambiguous bp: Initial: 270036281 bp After Masking: 238345347 bp Masked: 11.74 % -- Input Database Coverage: 400112116 bp out of 974517173 bp ( 41.06 % ) Sampling Time: 01:18:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23150610 Comparison Time: 132:27:16 (hh:mm:ss) Elapsed Time, 229297 HSPs Collected Number of families returned by RECON: 63626 Round Time: 135:51:54 (hh:mm:ss) Elapsed Time : 242 families discovered. RepeatScout/RECON discovery complete: 410 families found Classification Time: 01:25:18 (hh:mm:ss) Elapsed Time Program Time: 156:10:40 (hh:mm:ss) Elapsed Time