RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.Vy4Avl/RM_4114721.WedNov130636322024 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: 1731508592 Database = /scratch/tmp/rModeler.Vy4Avl/GCA_963989245.1_fNanAnt1.1 - Sequences = 1177 - Bases = 1085794659 - N50 = 75092094 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 107158461-114812566 | [ 1 ] 99504357-107158461 | [ ] 91850252-99504356 | [ ] 84196148-91850252 | [ 2 ] 76542044-84196148 | [ 2 ] 68887939-76542043 | [ 1 ] 61233835-68887939 | [ 1 ] 53579730-61233834 | [ 1 ] 45925626-53579730 | [ 1 ] 38271522-45925626 | [ ] 30617417-38271521 | [ 6 ] 22963313-30617417 | [ 4 ] 15309208-22963312 | [ 1 ] 7655104-15309208 | [ ] 1000-7655104 |************************************************** [ 1157 ] Storage Throughput = excellent ( 1586.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030732 bp ( 40005240 non ambiguous ) - Num Contigs Represented = 85 - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:42 (hh:mm:ss) Elapsed Time Round Time: 00:18:44 (hh:mm:ss) Elapsed Time : 1038 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13335 repeats masked totaling 3286354 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027931 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10020531 bp After Masking: 5189572 bp Masked: 48.21 % -- Input Database Coverage: 10027931 bp out of 1085794659 bp ( 0.92 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 4184 HSPs Collected Number of families returned by RECON: 1163 Round Time: 00:04:37 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40334 repeats masked totaling 9522307 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042848 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 30024756 bp After Masking: 15841696 bp Masked: 47.24 % -- Input Database Coverage: 40070779 bp out of 1085794659 bp ( 3.69 % ) Sampling Time: 00:05:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:11:14 (hh:mm:ss) Elapsed Time, 39637 HSPs Collected Number of families returned by RECON: 4369 Round Time: 00:16:50 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 123339 repeats masked totaling 27749658 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90071233 bp Num Contigs Represented = 172 Non ambiguous bp: Initial: 90011499 bp After Masking: 47634358 bp Masked: 47.08 % -- Input Database Coverage: 130142012 bp out of 1085794659 bp ( 11.99 % ) Sampling Time: 00:15:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2653056 Comparison Time: 01:00:30 (hh:mm:ss) Elapsed Time, 330381 HSPs Collected Number of families returned by RECON: 13661 Round Time: 01:21:44 (hh:mm:ss) Elapsed Time : 536 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 440801 repeats masked totaling 100023864 bp(s). - TE Masking time 00:06:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270164552 bp Num Contigs Represented = 388 Non ambiguous bp: Initial: 270007135 bp After Masking: 127200087 bp Masked: 52.89 % -- Input Database Coverage: 400306564 bp out of 1085794659 bp ( 36.87 % ) Sampling Time: 00:48:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23960503 Comparison Time: 06:29:25 (hh:mm:ss) Elapsed Time, 1061404 HSPs Collected Number of families returned by RECON: 41827 Round Time: 07:47:38 (hh:mm:ss) Elapsed Time : 1477 families discovered. RepeatScout/RECON discovery complete: 3119 families found Classification Time: 01:24:42 (hh:mm:ss) Elapsed Time Program Time: 11:14:15 (hh:mm:ss) Elapsed Time