RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.b3wmps/RM_2748742.ThuNov142128272024 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: 1731648507 Database = /scratch/tmp/rModeler.b3wmps/GCA_964194135.1_mTalEur1.hap1.1 - Sequences = 464 - Bases = 2061000977 - N50 = 138790915 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 148175229-158759103 | [ 3 ] 137591355-148175228 | [ 3 ] 127007482-137591355 | [ 1 ] 116423608-127007481 | [ 3 ] 105839735-116423608 | [ ] 95255861-105839734 | [ 4 ] 84671988-95255861 | [ 2 ] 74088114-84671987 | [ ] 63504241-74088114 | [ ] 52920367-63504240 | [ ] 42336494-52920367 | [ 1 ] 31752620-42336493 | [ ] 21168747-31752620 | [ ] 10584873-21168746 | [ ] 1000-10584873 |************************************************** [ 447 ] Storage Throughput = excellent ( 1408.83 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037329 bp ( 40032729 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:16 (hh:mm:ss) Elapsed Time Round Time: 00:15:09 (hh:mm:ss) Elapsed Time : 195 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10129 repeats masked totaling 2429029 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024541 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10022741 bp After Masking: 7450129 bp Masked: 25.67 % -- Input Database Coverage: 10024541 bp out of 2061000977 bp ( 0.49 % ) Sampling Time: 00:00:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:28 (hh:mm:ss) Elapsed Time, 14833 HSPs Collected Number of families returned by RECON: 640 Round Time: 00:04:44 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32070 repeats masked totaling 7877227 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012786 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30009986 bp After Masking: 21926868 bp Masked: 26.93 % -- Input Database Coverage: 40037327 bp out of 2061000977 bp ( 1.94 % ) Sampling Time: 00:01:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:13:47 (hh:mm:ss) Elapsed Time, 27727 HSPs Collected Number of families returned by RECON: 2670 Round Time: 00:16:15 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111842 repeats masked totaling 25455427 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043667 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90035267 bp After Masking: 63492940 bp Masked: 29.48 % -- Input Database Coverage: 130080994 bp out of 2061000977 bp ( 6.31 % ) Sampling Time: 00:05:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 01:14:37 (hh:mm:ss) Elapsed Time, 81976 HSPs Collected Number of families returned by RECON: 8062 Round Time: 01:22:00 (hh:mm:ss) Elapsed Time : 174 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 369020 repeats masked totaling 83619664 bp(s). - TE Masking time 00:02:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041703 bp Num Contigs Represented = 129 Non ambiguous bp: Initial: 270010399 bp After Masking: 182917398 bp Masked: 32.26 % -- Input Database Coverage: 400122697 bp out of 2061000977 bp ( 19.41 % ) Sampling Time: 00:17:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22994371 Comparison Time: 09:26:59 (hh:mm:ss) Elapsed Time, 236640 HSPs Collected Number of families returned by RECON: 33733 Round Time: 09:55:21 (hh:mm:ss) Elapsed Time : 394 families discovered. RepeatScout/RECON discovery complete: 836 families found Classification Time: 00:21:45 (hh:mm:ss) Elapsed Time Program Time: 12:15:14 (hh:mm:ss) Elapsed Time