RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.V5E3Q3/RM_2112023.MonDec90243292024 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: 1733741008 Database = /data/tmp/rModeler.V5E3Q3/GCA_043290065.1_mRhyPet1.hap2 - Sequences = 314 - Bases = 5331151070 - N50 = 601969587 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 824386281-883270168 | [ 1 ] 765502394-824386280 | [ ] 706618508-765502394 | [ 1 ] 647734621-706618507 | [ ] 588850735-647734621 | [ 1 ] 529966848-588850734 | [ 2 ] 471082962-529966848 | [ 2 ] 412199075-471082961 | [ ] 353315189-412199075 | [ ] 294431302-353315188 | [ 1 ] 235547416-294431302 | [ 1 ] 176663529-235547415 | [ 1 ] 117779643-176663529 | [ 1 ] 58895756-117779642 | [ ] 11870-58895756 |************************************************** [ 303 ] Storage Throughput = excellent ( 1134.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035127 bp ( 40034927 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:11:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:42 (hh:mm:ss) Elapsed Time Round Time: 00:57:40 (hh:mm:ss) Elapsed Time : 281 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:41 (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... 25439 repeats masked totaling 6641233 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004354 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 10004354 bp After Masking: 3293054 bp Masked: 67.08 % -- Input Database Coverage: 10004354 bp out of 5331151070 bp ( 0.19 % ) Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:08 (hh:mm:ss) Elapsed Time, 2853 HSPs Collected Number of families returned by RECON: 349 Round Time: 00:07:52 (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 : 00:07:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75201 repeats masked totaling 19970727 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030693 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30030493 bp After Masking: 9599500 bp Masked: 68.03 % -- Input Database Coverage: 40035047 bp out of 5331151070 bp ( 0.75 % ) Sampling Time: 00:09:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:17:03 (hh:mm:ss) Elapsed Time, 12922 HSPs Collected Number of families returned by RECON: 1156 Round Time: 00:27:34 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:23:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 233252 repeats masked totaling 61548241 bp(s). - TE Masking time 00:01:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004915 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 90002115 bp After Masking: 27252084 bp Masked: 69.72 % -- Input Database Coverage: 130039962 bp out of 5331151070 bp ( 2.44 % ) Sampling Time: 00:27:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:40:14 (hh:mm:ss) Elapsed Time, 67697 HSPs Collected Number of families returned by RECON: 3760 Round Time: 02:18:25 (hh:mm:ss) Elapsed Time : 112 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:08:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 725738 repeats masked totaling 189586116 bp(s). - TE Masking time 00:06:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270035206 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 270029814 bp After Masking: 76820185 bp Masked: 71.55 % -- Input Database Coverage: 400075168 bp out of 5331151070 bp ( 7.50 % ) Sampling Time: 01:24:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 12:23:12 (hh:mm:ss) Elapsed Time, 155979 HSPs Collected Number of families returned by RECON: 12090 Round Time: 14:04:21 (hh:mm:ss) Elapsed Time : 254 families discovered. RepeatScout/RECON discovery complete: 682 families found Classification Time: 00:21:02 (hh:mm:ss) Elapsed Time Program Time: 18:16:54 (hh:mm:ss) Elapsed Time