RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.R7qbvY/RM_3790564.MonJul221040572024 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: 1721670043 Database = /dev/shm/rModeler.R7qbvY/GCF_022655615.1_HZAU_PFXX_2.0 - Sequences = 517 - Bases = 712016913 - N50 = 27792978 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 48994813-52494416 | [ 1 ] 45495211-48994813 | [ ] 41995609-45495211 | [ 1 ] 38496007-41995609 | [ ] 34996405-38496007 | [ ] 31496802-34996404 | [ 4 ] 27997200-31496802 | [ 3 ] 24497598-27997200 | [ 6 ] 20997996-24497598 | [ 7 ] 17498394-20997996 | [ 3 ] 13998791-17498393 | [ 1 ] 10499189-13998791 | [ ] 6999587-10499189 | [ ] 3499985-6999587 | [ ] 383-3499985 |************************************************** [ 491 ] Storage Throughput = good ( 786.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40050061 bp ( 40037913 non ambiguous ) - Num Contigs Represented = 64 - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:37 (hh:mm:ss) Elapsed Time Round Time: 00:40:23 (hh:mm:ss) Elapsed Time : 459 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9108 repeats masked totaling 1596553 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027643 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10023494 bp After Masking: 7631339 bp Masked: 23.87 % -- Input Database Coverage: 10027643 bp out of 712016913 bp ( 1.41 % ) Sampling Time: 00:02:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 01:05:02 (hh:mm:ss) Elapsed Time, 5288 HSPs Collected Number of families returned by RECON: 1080 Round Time: 01:08:52 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28475 repeats masked totaling 5258596 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022338 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30014339 bp After Masking: 21809048 bp Masked: 27.34 % -- Input Database Coverage: 40049981 bp out of 712016913 bp ( 5.62 % ) Sampling Time: 00:08:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296065 Comparison Time: 03:00:04 (hh:mm:ss) Elapsed Time, 30153 HSPs Collected Number of families returned by RECON: 3972 Round Time: 03:14:12 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 92670 repeats masked totaling 16482796 bp(s). - TE Masking time 00:02:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90079808 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 90023757 bp After Masking: 64679426 bp Masked: 28.15 % -- Input Database Coverage: 130129789 bp out of 712016913 bp ( 18.28 % ) Sampling Time: 00:25:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2662278 Comparison Time: 09:37:36 (hh:mm:ss) Elapsed Time, 186206 HSPs Collected Number of families returned by RECON: 15262 Round Time: 10:24:37 (hh:mm:ss) Elapsed Time : 363 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:04:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 329106 repeats masked totaling 60073080 bp(s). - TE Masking time 00:08:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270152599 bp Num Contigs Represented = 211 Non ambiguous bp: Initial: 270011366 bp After Masking: 183572448 bp Masked: 32.01 % -- Input Database Coverage: 400282388 bp out of 712016913 bp ( 56.22 % ) Sampling Time: 01:17:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23891328 Comparison Time: 50:56:39 (hh:mm:ss) Elapsed Time, 690236 HSPs Collected Number of families returned by RECON: 53424 Round Time: 54:18:26 (hh:mm:ss) Elapsed Time : 967 families discovered. RepeatScout/RECON discovery complete: 1878 families found Classification Time: 01:37:31 (hh:mm:ss) Elapsed Time Program Time: 71:24:02 (hh:mm:ss) Elapsed Time