RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Vowsnc/RM_12137.WedJan101935372024 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: 1704944136 Database = /dev/shm/rModeler.Vowsnc/GCA_020740715.1_mJacJac1.pat.decon - Sequences = 508 - Bases = 2595216862 - N50 = 134725597 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 197320976-211415189 | [ 2 ] 183226763-197320975 | [ ] 169132551-183226763 | [ 2 ] 155038338-169132550 | [ 1 ] 140944126-155038338 | [ 1 ] 126849913-140944125 | [ 1 ] 112755701-126849913 | [ 1 ] 98661488-112755700 | [ 2 ] 84567276-98661488 | [ 1 ] 70473063-84567275 | [ 2 ] 56378851-70473063 | [ 3 ] 42284638-56378850 | [ 3 ] 28190426-42284638 | [ 6 ] 14096213-28190425 | [ 5 ] 2001-14096213 |************************************************** [ 478 ] Storage Throughput = excellent ( 1131.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43974026 bp ( 40017859 non ambiguous ) - Num Contigs Represented = 65 - Sequence extraction : 00:03:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:51 (hh:mm:ss) Elapsed Time Round Time: 00:29:40 (hh:mm:ss) Elapsed Time : 280 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21523 repeats masked totaling 4117390 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11009065 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10019903 bp After Masking: 5711089 bp Masked: 43.00 % -- Input Database Coverage: 11009065 bp out of 2595216862 bp ( 0.42 % ) Sampling Time: 00:01:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 37950 Comparison Time: 00:05:34 (hh:mm:ss) Elapsed Time, 3703 HSPs Collected Number of families returned by RECON: 573 Round Time: 00:07:36 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62234 repeats masked totaling 12412550 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 33004960 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30037955 bp After Masking: 17097764 bp Masked: 43.08 % -- Input Database Coverage: 44014025 bp out of 2595216862 bp ( 1.70 % ) Sampling Time: 00:04:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 343206 Comparison Time: 00:29:00 (hh:mm:ss) Elapsed Time, 38483 HSPs Collected Number of families returned by RECON: 1945 Round Time: 00:34:19 (hh:mm:ss) Elapsed Time : 49 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 198313 repeats masked totaling 38958580 bp(s). - TE Masking time 00:01:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 96720866 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 90034348 bp After Masking: 49803164 bp Masked: 44.68 % -- Input Database Coverage: 140734891 bp out of 2595216862 bp ( 5.42 % ) Sampling Time: 00:12:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2936676 Comparison Time: 03:12:30 (hh:mm:ss) Elapsed Time, 334026 HSPs Collected Number of families returned by RECON: 6442 Round Time: 03:29:03 (hh:mm:ss) Elapsed Time : 155 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 638801 repeats masked totaling 120378807 bp(s). - TE Masking time 00:07:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 291452750 bp Num Contigs Represented = 131 Non ambiguous bp: Initial: 270037780 bp After Masking: 145423633 bp Masked: 46.15 % -- Input Database Coverage: 432187641 bp out of 2595216862 bp ( 16.65 % ) Sampling Time: 00:39:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26772903 Comparison Time: 24:18:12 (hh:mm:ss) Elapsed Time, 918605 HSPs Collected Number of families returned by RECON: 27291 Round Time: 25:20:12 (hh:mm:ss) Elapsed Time : 353 families discovered. RepeatScout/RECON discovery complete: 850 families found Classification Time: 00:29:49 (hh:mm:ss) Elapsed Time Program Time: 30:30:39 (hh:mm:ss) Elapsed Time