RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.CkASoE/RM_26553.WedJul100944362024 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: 1720629875 Database = /dev/shm/rModeler.CkASoE/GCF_001952655.1_M_albus_1.0 - Sequences = 20622 - Bases = 684144148 - N50 = 2109581 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 10897768-11676166 | [ 1 ] 10119370-10897767 | [ 1 ] 9340972-10119369 | [ ] 8562575-9340972 | [ 2 ] 7784177-8562574 | [ ] 7005779-7784176 | [ 3 ] 6227381-7005778 | [ 4 ] 5448984-6227381 | [ 3 ] 4670586-5448983 | [ 4 ] 3892188-4670585 | [ 16 ] 3113790-3892187 | [ 16 ] 2335393-3113790 | [ 26 ] 1556995-2335392 | [ 50 ] 778597-1556994 | [ 125 ] 200-778597 |************************************************** [ 20371 ] Storage Throughput = excellent ( 1005.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43441821 bp ( 40028899 non ambiguous ) - Num Contigs Represented = 1653 - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:27 (hh:mm:ss) Elapsed Time Round Time: 00:24:12 (hh:mm:ss) Elapsed Time : 645 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9520 repeats masked totaling 1666884 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10837021 bp Num Contigs Represented = 514 Non ambiguous bp: Initial: 10028810 bp After Masking: 8327727 bp Masked: 16.96 % -- Input Database Coverage: 10837021 bp out of 684144148 bp ( 1.58 % ) Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 179101 Comparison Time: 00:07:43 (hh:mm:ss) Elapsed Time, 10287 HSPs Collected Number of families returned by RECON: 1592 Round Time: 00:08:37 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28780 repeats masked totaling 5084165 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32604796 bp Num Contigs Represented = 1276 Non ambiguous bp: Initial: 30000085 bp After Masking: 24803063 bp Masked: 17.32 % -- Input Database Coverage: 43441817 bp out of 684144148 bp ( 6.35 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1544403 Comparison Time: 01:45:03 (hh:mm:ss) Elapsed Time, 54332 HSPs Collected Number of families returned by RECON: 5488 Round Time: 01:50:04 (hh:mm:ss) Elapsed Time : 136 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:20 (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... 100866 repeats masked totaling 17950836 bp(s). - TE Masking time 00:02:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 97980202 bp Num Contigs Represented = 3276 Non ambiguous bp: Initial: 90017004 bp After Masking: 71667847 bp Masked: 20.38 % -- Input Database Coverage: 141422019 bp out of 684144148 bp ( 20.67 % ) Sampling Time: 00:04:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 13616371 Comparison Time: 04:42:12 (hh:mm:ss) Elapsed Time, 259064 HSPs Collected Number of families returned by RECON: 19274 Round Time: 05:02:41 (hh:mm:ss) Elapsed Time : 469 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 363884 repeats masked totaling 65787492 bp(s). - TE Masking time 00:10:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 292976430 bp Num Contigs Represented = 9125 Non ambiguous bp: Initial: 270007114 bp After Masking: 203111655 bp Masked: 24.78 % -- Input Database Coverage: 434398449 bp out of 684144148 bp ( 63.50 % ) Sampling Time: 00:18:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 124149403 Comparison Time: 34:15:36 (hh:mm:ss) Elapsed Time, 736774 HSPs Collected Number of families returned by RECON: 74569 Round Time: 36:57:58 (hh:mm:ss) Elapsed Time : 1130 families discovered. RepeatScout/RECON discovery complete: 2394 families found Classification Time: 01:33:25 (hh:mm:ss) Elapsed Time Program Time: 45:56:57 (hh:mm:ss) Elapsed Time