RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.H8RlKw/RM_2841315.SatNov161655002024 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: 1731804900 Database = /scratch/tmp/rModeler.H8RlKw/GCA_964188345.1_bAnaPla2.hap1.1 - Sequences = 936 - Bases = 1300248985 - N50 = 85226422 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 193516319-207338842 | [ 1 ] 179693796-193516318 | [ ] 165871273-179693795 | [ ] 152048750-165871272 | [ 1 ] 138226228-152048750 | [ ] 124403705-138226227 | [ ] 110581182-124403704 | [ 1 ] 96758659-110581181 | [ ] 82936136-96758658 | [ 1 ] 69113614-82936136 | [ 2 ] 55291091-69113613 | [ ] 41468568-55291090 | [ 1 ] 27646045-41468567 | [ 3 ] 13823522-27646044 | [ 11 ] 1000-13823522 |************************************************** [ 915 ] Storage Throughput = excellent ( 1584.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038424 bp ( 40034424 non ambiguous ) - Num Contigs Represented = 106 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:36 (hh:mm:ss) Elapsed Time Round Time: 00:11:11 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2001 repeats masked totaling 733232 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10016781 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10016381 bp After Masking: 8526616 bp Masked: 14.87 % -- Input Database Coverage: 10016781 bp out of 1300248985 bp ( 0.77 % ) Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:03:29 (hh:mm:ss) Elapsed Time, 4357 HSPs Collected Number of families returned by RECON: 205 Round Time: 00:04:23 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6438 repeats masked totaling 2283275 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021640 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 30018040 bp After Masking: 25158364 bp Masked: 16.19 % -- Input Database Coverage: 40038421 bp out of 1300248985 bp ( 3.08 % ) Sampling Time: 00:03:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:16:04 (hh:mm:ss) Elapsed Time, 38872 HSPs Collected Number of families returned by RECON: 1503 Round Time: 00:20:55 (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 : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21172 repeats masked totaling 8165468 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90047384 bp Num Contigs Represented = 196 Non ambiguous bp: Initial: 90039848 bp After Masking: 74345487 bp Masked: 17.43 % -- Input Database Coverage: 130085805 bp out of 1300248985 bp ( 10.00 % ) Sampling Time: 00:11:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 01:48:26 (hh:mm:ss) Elapsed Time, 198369 HSPs Collected Number of families returned by RECON: 8529 Round Time: 02:03:01 (hh:mm:ss) Elapsed Time : 84 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 78511 repeats masked totaling 30214155 bp(s). - TE Masking time 00:02:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270026257 bp Num Contigs Represented = 398 Non ambiguous bp: Initial: 270001257 bp After Masking: 218146593 bp Masked: 19.21 % -- Input Database Coverage: 400112062 bp out of 1300248985 bp ( 30.77 % ) Sampling Time: 00:28:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23403061 Comparison Time: 13:49:07 (hh:mm:ss) Elapsed Time, 3089958 HSPs Collected Number of families returned by RECON: 53091 Round Time: 14:39:40 (hh:mm:ss) Elapsed Time : 250 families discovered. RepeatScout/RECON discovery complete: 439 families found Classification Time: 00:30:01 (hh:mm:ss) Elapsed Time Program Time: 17:49:11 (hh:mm:ss) Elapsed Time