RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.UdoOYF/RM_2127588.MonNov181443142024 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: 1731969794 Database = /scratch/tmp/rModeler.UdoOYF/GCA_964146895.1_mMinSch1.hap1.1 - Sequences = 265 - Bases = 1852127854 - N50 = 92790464 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 188825795-202313281 | [ 2 ] 175338310-188825795 | [ ] 161850824-175338309 | [ ] 148363339-161850824 | [ ] 134875854-148363339 | [ ] 121388368-134875853 | [ ] 107900883-121388368 | [ ] 94413397-107900882 | [ 3 ] 80925912-94413397 |* [ 6 ] 67438427-80925912 | [ 2 ] 53950941-67438426 | [ 3 ] 40463456-53950941 | [ 3 ] 26975970-40463455 | [ 2 ] 13488485-26975970 | [ 3 ] 1000-13488485 |************************************************** [ 241 ] Storage Throughput = excellent ( 1472.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036327 bp ( 40029127 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:34 (hh:mm:ss) Elapsed Time Round Time: 00:11:13 (hh:mm:ss) Elapsed Time : 169 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7725 repeats masked totaling 1624531 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041162 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10038962 bp After Masking: 7997816 bp Masked: 20.33 % -- Input Database Coverage: 10041162 bp out of 1852127854 bp ( 0.54 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:00 (hh:mm:ss) Elapsed Time, 6762 HSPs Collected Number of families returned by RECON: 965 Round Time: 00:04:17 (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 : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27643 repeats masked totaling 6108070 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035086 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30030086 bp After Masking: 22683674 bp Masked: 24.46 % -- Input Database Coverage: 40076248 bp out of 1852127854 bp ( 2.16 % ) Sampling Time: 00:03:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:13:47 (hh:mm:ss) Elapsed Time, 25734 HSPs Collected Number of families returned by RECON: 2727 Round Time: 00:17:21 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 95671 repeats masked totaling 20960423 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90049493 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 90034496 bp After Masking: 65500967 bp Masked: 27.25 % -- Input Database Coverage: 130125741 bp out of 1852127854 bp ( 7.03 % ) Sampling Time: 00:08:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:20:33 (hh:mm:ss) Elapsed Time, 186578 HSPs Collected Number of families returned by RECON: 9350 Round Time: 01:31:18 (hh:mm:ss) Elapsed Time : 192 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 324862 repeats masked totaling 70979084 bp(s). - TE Masking time 00:01:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270043914 bp Num Contigs Represented = 112 Non ambiguous bp: Initial: 270004891 bp After Masking: 188214465 bp Masked: 30.29 % -- Input Database Coverage: 400169655 bp out of 1852127854 bp ( 21.61 % ) Sampling Time: 00:30:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 08:47:33 (hh:mm:ss) Elapsed Time, 807970 HSPs Collected Number of families returned by RECON: 38998 Round Time: 09:32:15 (hh:mm:ss) Elapsed Time : 327 families discovered. RepeatScout/RECON discovery complete: 775 families found Classification Time: 00:14:58 (hh:mm:ss) Elapsed Time Program Time: 11:51:22 (hh:mm:ss) Elapsed Time