RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.UMbNUI/RM_1983845.FriJul181029582025 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: 1752859797 Database = /dev/shm/rModeler.UMbNUI/GCA_047512175.1_mMarFla1.hap2 - Sequences = 329 - Bases = 2467036054 - N50 = 159701540 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201481270-215871762 | [ 2 ] 187090778-201481269 | [ ] 172700286-187090777 | [ 1 ] 158309794-172700285 | [ 3 ] 143919302-158309793 | [ ] 129528810-143919301 | [ 2 ] 115138318-129528809 | [ 3 ] 100747826-115138317 | [ 1 ] 86357334-100747825 | [ 2 ] 71966842-86357333 | [ 3 ] 57576350-71966841 | [ 1 ] 43185858-57576349 | [ ] 28795366-43185857 | [ 1 ] 14404874-28795365 | [ 1 ] 14383-14404874 |************************************************** [ 309 ] Storage Throughput = excellent ( 1188.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034747 bp ( 40034547 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:02:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:54 (hh:mm:ss) Elapsed Time Round Time: 00:33:24 (hh:mm:ss) Elapsed Time : 216 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11201 repeats masked totaling 2289857 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002918 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10002918 bp After Masking: 7589358 bp Masked: 24.13 % -- Input Database Coverage: 10002918 bp out of 2467036054 bp ( 0.41 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:15 (hh:mm:ss) Elapsed Time, 7467 HSPs Collected Number of families returned by RECON: 856 Round Time: 00:06:51 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35175 repeats masked totaling 7075109 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031827 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30031627 bp After Masking: 22631592 bp Masked: 24.64 % -- Input Database Coverage: 40034745 bp out of 2467036054 bp ( 1.62 % ) Sampling Time: 00:03:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:30:34 (hh:mm:ss) Elapsed Time, 25563 HSPs Collected Number of families returned by RECON: 2827 Round Time: 00:35:23 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 124190 repeats masked totaling 24869858 bp(s). - TE Masking time 00:01:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038049 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 90036049 bp After Masking: 63923273 bp Masked: 29.00 % -- Input Database Coverage: 130072794 bp out of 2467036054 bp ( 5.27 % ) Sampling Time: 00:12:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 03:39:17 (hh:mm:ss) Elapsed Time, 148369 HSPs Collected Number of families returned by RECON: 8505 Round Time: 03:56:53 (hh:mm:ss) Elapsed Time : 166 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 418805 repeats masked totaling 85051016 bp(s). - TE Masking time 00:06:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270018868 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 270012468 bp After Masking: 181413877 bp Masked: 32.81 % -- Input Database Coverage: 400091662 bp out of 2467036054 bp ( 16.22 % ) Sampling Time: 00:39:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22906296 Comparison Time: 28:23:38 (hh:mm:ss) Elapsed Time, 945127 HSPs Collected Number of families returned by RECON: 36777 Round Time: 29:40:52 (hh:mm:ss) Elapsed Time : 402 families discovered. RepeatScout/RECON discovery complete: 858 families found Classification Time: 00:52:05 (hh:mm:ss) Elapsed Time Program Time: 35:45:28 (hh:mm:ss) Elapsed Time