RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.Xl7sJY/RM_392628.WedNov132350312024 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: 1731570631 Database = /scratch/tmp/rModeler.Xl7sJY/GCA_964059595.1_bBucCla1.1 - Sequences = 538 - Bases = 1190938797 - N50 = 77850840 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 121933172-130642613 | [ 1 ] 113223731-121933171 | [ 1 ] 104514290-113223730 | [ ] 95804849-104514289 | [ 1 ] 87095408-95804848 | [ 1 ] 78385967-87095407 | [ 1 ] 69676526-78385966 | [ 1 ] 60967086-69676526 | [ 2 ] 52257645-60967085 | [ ] 43548204-52257644 | [ ] 34838763-43548203 | [ 2 ] 26129322-34838762 | [ 2 ] 17419881-26129321 | [ 6 ] 8710440-17419880 | [ 6 ] 1000-8710440 |************************************************** [ 514 ] Storage Throughput = excellent ( 1566.46 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039803 bp ( 40036403 non ambiguous ) - Num Contigs Represented = 83 - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:02 (hh:mm:ss) Elapsed Time Round Time: 00:14:37 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1961 repeats masked totaling 792655 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030336 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10029936 bp After Masking: 9044562 bp Masked: 9.82 % -- Input Database Coverage: 10030336 bp out of 1190938797 bp ( 0.84 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:36 (hh:mm:ss) Elapsed Time, 550 HSPs Collected Number of families returned by RECON: 215 Round Time: 00:04:48 (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 : 00:00:30 (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... 6346 repeats masked totaling 2913051 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009387 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 30006387 bp After Masking: 26387856 bp Masked: 12.06 % -- Input Database Coverage: 40039723 bp out of 1190938797 bp ( 3.36 % ) Sampling Time: 00:03:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:18:25 (hh:mm:ss) Elapsed Time, 6791 HSPs Collected Number of families returned by RECON: 1535 Round Time: 00:21:56 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19488 repeats masked totaling 8577073 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025683 bp Num Contigs Represented = 132 Non ambiguous bp: Initial: 90017809 bp After Masking: 79028582 bp Masked: 12.21 % -- Input Database Coverage: 130065406 bp out of 1190938797 bp ( 10.92 % ) Sampling Time: 00:13:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 02:23:47 (hh:mm:ss) Elapsed Time, 48234 HSPs Collected Number of families returned by RECON: 9453 Round Time: 02:39:16 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68919 repeats masked totaling 30034367 bp(s). - TE Masking time 00:01:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270030389 bp Num Contigs Represented = 291 Non ambiguous bp: Initial: 270008858 bp After Masking: 232390072 bp Masked: 13.93 % -- Input Database Coverage: 400095795 bp out of 1190938797 bp ( 33.59 % ) Sampling Time: 00:43:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23232336 Comparison Time: 16:13:48 (hh:mm:ss) Elapsed Time, 315995 HSPs Collected Number of families returned by RECON: 61081 Round Time: 17:17:37 (hh:mm:ss) Elapsed Time : 233 families discovered. RepeatScout/RECON discovery complete: 386 families found Classification Time: 00:15:00 (hh:mm:ss) Elapsed Time Program Time: 20:53:14 (hh:mm:ss) Elapsed Time