RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.35tAMg/RM_5978.WedJan101935382024 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: 1704944137 Database = /dev/shm/rModeler.35tAMg/GCA_024803745.1_mThoBot1.0.p - Sequences = 2792 - Bases = 2845630888 - N50 = 26618111 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 76030251-81460496 | [ 2 ] 70600007-76030251 | [ ] 65169763-70600007 | [ 6 ] 59739519-65169763 | [ 3 ] 54309275-59739519 | [ 3 ] 48879031-54309275 | [ 1 ] 43448787-48879031 | [ 2 ] 38018542-43448786 | [ 1 ] 32588298-38018542 | [ 4 ] 27158054-32588298 | [ 4 ] 21727810-27158054 | [ 5 ] 16297566-21727810 | [ 5 ] 10867322-16297566 | [ 4 ] 5437078-10867322 | [ 14 ] 6834-5437078 |************************************************** [ 2738 ] Storage Throughput = excellent ( 1130.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40004206 bp ( 40004206 non ambiguous ) - Num Contigs Represented = 370 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:52 (hh:mm:ss) Elapsed Time Round Time: 01:21:05 (hh:mm:ss) Elapsed Time : 244 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15506 repeats masked totaling 4009733 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014060 bp Num Contigs Represented = 154 Non ambiguous bp: Initial: 10014060 bp After Masking: 4053083 bp Masked: 59.53 % -- Input Database Coverage: 10014060 bp out of 2845630888 bp ( 0.35 % ) Sampling Time: 00:19:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:04:49 (hh:mm:ss) Elapsed Time, 1403 HSPs Collected Number of families returned by RECON: 286 Round Time: 00:24:07 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50078 repeats masked totaling 12110939 bp(s). - TE Masking time 00:02:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030066 bp Num Contigs Represented = 291 Non ambiguous bp: Initial: 30030066 bp After Masking: 13206563 bp Masked: 56.02 % -- Input Database Coverage: 40044126 bp out of 2845630888 bp ( 1.41 % ) Sampling Time: 00:45:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:22:33 (hh:mm:ss) Elapsed Time, 34883 HSPs Collected Number of families returned by RECON: 1166 Round Time: 01:08:53 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:21:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149853 repeats masked totaling 35786632 bp(s). - TE Masking time 00:07:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013769 bp Num Contigs Represented = 654 Non ambiguous bp: Initial: 90013369 bp After Masking: 38477320 bp Masked: 57.25 % -- Input Database Coverage: 130057895 bp out of 2845630888 bp ( 4.57 % ) Sampling Time: 02:30:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2630071 Comparison Time: 02:11:38 (hh:mm:ss) Elapsed Time, 458313 HSPs Collected Number of families returned by RECON: 3888 Round Time: 04:43:55 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 07:19:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 463373 repeats masked totaling 110753597 bp(s). - TE Masking time 00:23:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270001304 bp Num Contigs Represented = 1197 Non ambiguous bp: Initial: 270000604 bp After Masking: 112711206 bp Masked: 58.26 % -- Input Database Coverage: 400059199 bp out of 2845630888 bp ( 14.06 % ) Sampling Time: 07:47:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23636250 Comparison Time: 16:49:18 (hh:mm:ss) Elapsed Time, 4172524 HSPs Collected Number of families returned by RECON: 16186 Round Time: 25:15:07 (hh:mm:ss) Elapsed Time : 361 families discovered. RepeatScout/RECON discovery complete: 709 families found Classification Time: 01:14:59 (hh:mm:ss) Elapsed Time Program Time: 34:08:06 (hh:mm:ss) Elapsed Time