RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.8jzu40/RM_480988.WedApr231220062025 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: 1745436004 Database = /dev/shm/rModeler.8jzu40/GCA_048129235.1_fEpiMut1.hap1.cur.20240206 - Sequences = 386 - Bases = 1035398499 - N50 = 41832733 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 46347543-49657586 | [ 3 ] 43037500-46347542 | [ 7 ] 39727457-43037499 |* [ 8 ] 36417415-39727457 | [ 3 ] 33107372-36417414 | [ 2 ] 29797329-33107371 | [ ] 26487286-29797328 | [ ] 23177244-26487286 | [ ] 19867201-23177243 | [ 1 ] 16557158-19867200 | [ ] 13247115-16557157 | [ ] 9937073-13247115 | [ ] 6627030-9937072 | [ ] 3316987-6627029 | [ ] 6945-3316987 |************************************************** [ 362 ] Storage Throughput = excellent ( 1749.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40004075 bp ( 40004075 non ambiguous ) - Num Contigs Represented = 68 - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:51 (hh:mm:ss) Elapsed Time Round Time: 00:09:54 (hh:mm:ss) Elapsed Time : 941 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15868 repeats masked totaling 2300931 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029464 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10029464 bp After Masking: 7324722 bp Masked: 26.97 % -- Input Database Coverage: 10029464 bp out of 1035398499 bp ( 0.97 % ) Sampling Time: 00:00:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:00 (hh:mm:ss) Elapsed Time, 12522 HSPs Collected Number of families returned by RECON: 2099 Round Time: 00:03:53 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48158 repeats masked totaling 6800561 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014535 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30014535 bp After Masking: 21506213 bp Masked: 28.35 % -- Input Database Coverage: 40043999 bp out of 1035398499 bp ( 3.87 % ) Sampling Time: 00:02:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:13:15 (hh:mm:ss) Elapsed Time, 99009 HSPs Collected Number of families returned by RECON: 6643 Round Time: 00:17:01 (hh:mm:ss) Elapsed Time : 223 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 164125 repeats masked totaling 24216776 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90006627 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 90006227 bp After Masking: 61608607 bp Masked: 31.55 % -- Input Database Coverage: 130050626 bp out of 1035398499 bp ( 12.56 % ) Sampling Time: 00:05:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 01:14:44 (hh:mm:ss) Elapsed Time, 436182 HSPs Collected Number of families returned by RECON: 18642 Round Time: 01:28:25 (hh:mm:ss) Elapsed Time : 782 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 593917 repeats masked totaling 92195754 bp(s). - TE Masking time 00:04:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023090 bp Num Contigs Represented = 190 Non ambiguous bp: Initial: 270022290 bp After Masking: 164527735 bp Masked: 39.07 % -- Input Database Coverage: 400073716 bp out of 1035398499 bp ( 38.64 % ) Sampling Time: 00:22:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23028291 Comparison Time: 07:54:07 (hh:mm:ss) Elapsed Time, 1610322 HSPs Collected Number of families returned by RECON: 56497 Round Time: 08:54:41 (hh:mm:ss) Elapsed Time : 1582 families discovered. RepeatScout/RECON discovery complete: 3551 families found Classification Time: 01:01:58 (hh:mm:ss) Elapsed Time Program Time: 11:55:52 (hh:mm:ss) Elapsed Time