RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.vSunEC/RM_1144039.TueNov121147292024 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: 1731440848 Database = /scratch/tmp/rModeler.vSunEC/GCA_964106545.1_mNeoVis2.hap1.1 - Sequences = 435 - Bases = 2697147479 - N50 = 224197019 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 303949410-325660011 | [ 1 ] 282238809-303949409 | [ ] 260528208-282238808 | [ ] 238817608-260528208 | [ 2 ] 217107007-238817607 | [ 3 ] 195396406-217107006 | [ 1 ] 173685805-195396405 | [ ] 151975205-173685805 | [ 1 ] 130264604-151975204 | [ 4 ] 108554003-130264603 | [ ] 86843402-108554002 | [ 1 ] 65132802-86843402 | [ 1 ] 43422201-65132801 | [ 1 ] 21711600-43422200 | [ ] 1000-21711600 |************************************************** [ 420 ] Storage Throughput = excellent ( 1588.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041157 bp ( 40035757 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:28 (hh:mm:ss) Elapsed Time Round Time: 00:12:48 (hh:mm:ss) Elapsed Time : 144 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12068 repeats masked totaling 2995344 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025425 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10023825 bp After Masking: 6968301 bp Masked: 30.48 % -- Input Database Coverage: 10025425 bp out of 2697147479 bp ( 0.37 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:14 (hh:mm:ss) Elapsed Time, 13615 HSPs Collected Number of families returned by RECON: 765 Round Time: 00:04:12 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39478 repeats masked totaling 9373016 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015652 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30011852 bp After Masking: 20493189 bp Masked: 31.72 % -- Input Database Coverage: 40041077 bp out of 2697147479 bp ( 1.48 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:14:05 (hh:mm:ss) Elapsed Time, 51940 HSPs Collected Number of families returned by RECON: 2306 Round Time: 00:17:05 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 129653 repeats masked totaling 31056296 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022435 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 90002435 bp After Masking: 58426486 bp Masked: 35.08 % -- Input Database Coverage: 130063512 bp out of 2697147479 bp ( 4.82 % ) Sampling Time: 00:07:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 01:20:59 (hh:mm:ss) Elapsed Time, 406929 HSPs Collected Number of families returned by RECON: 7524 Round Time: 01:30:14 (hh:mm:ss) Elapsed Time : 116 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 426115 repeats masked totaling 98444413 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270095942 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 270037266 bp After Masking: 170134935 bp Masked: 37.00 % -- Input Database Coverage: 400159454 bp out of 2697147479 bp ( 14.84 % ) Sampling Time: 00:20:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22960476 Comparison Time: 09:19:12 (hh:mm:ss) Elapsed Time, 3426506 HSPs Collected Number of families returned by RECON: 34067 Round Time: 09:55:23 (hh:mm:ss) Elapsed Time : 357 families discovered. RepeatScout/RECON discovery complete: 698 families found Classification Time: 00:17:03 (hh:mm:ss) Elapsed Time Program Time: 12:16:45 (hh:mm:ss) Elapsed Time