RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.CVJFGp/RM_1971416.SunDec81406072024 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: 1733695567 Database = /scratch/tmp/rModeler.CVJFGp/GCA_964106635.2_rPodPit1.hap2.2 - Sequences = 183 - Bases = 1417079496 - N50 = 99089829 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 130462611-139781298 | [ 1 ] 121143924-130462610 | [ 2 ] 111825238-121143924 | [ ] 102506551-111825237 | [ 1 ] 93187865-102506551 | [ 2 ] 83869178-93187864 | [ 2 ] 74550492-83869178 | [ 2 ] 65231805-74550491 | [ ] 55913119-65231805 | [ 2 ] 46594432-55913118 | [ 2 ] 37275746-46594432 | [ 3 ] 27957059-37275745 | [ ] 18638373-27957059 | [ ] 9319686-18638372 | [ 1 ] 1000-9319686 |************************************************** [ 165 ] Storage Throughput = excellent ( 1508.52 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021180 bp ( 40013180 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:43 (hh:mm:ss) Elapsed Time Round Time: 00:10:26 (hh:mm:ss) Elapsed Time : 542 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 00:00:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17248 repeats masked totaling 3225452 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038184 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10036984 bp After Masking: 6686595 bp Masked: 33.38 % -- Input Database Coverage: 10038184 bp out of 1417079496 bp ( 0.71 % ) Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:53 (hh:mm:ss) Elapsed Time, 11306 HSPs Collected Number of families returned by RECON: 1406 Round Time: 00:03:35 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53070 repeats masked totaling 10242596 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022989 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30016189 bp After Masking: 19451042 bp Masked: 35.20 % -- Input Database Coverage: 40061173 bp out of 1417079496 bp ( 2.83 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:12:16 (hh:mm:ss) Elapsed Time, 46985 HSPs Collected Number of families returned by RECON: 4270 Round Time: 00:14:28 (hh:mm:ss) Elapsed Time : 112 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 174115 repeats masked totaling 32915455 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90046785 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90026573 bp After Masking: 55837203 bp Masked: 37.98 % -- Input Database Coverage: 130107958 bp out of 1417079496 bp ( 9.18 % ) Sampling Time: 00:04:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 01:07:34 (hh:mm:ss) Elapsed Time, 192392 HSPs Collected Number of families returned by RECON: 13932 Round Time: 01:15:53 (hh:mm:ss) Elapsed Time : 443 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 588691 repeats masked totaling 107711398 bp(s). - TE Masking time 00:02:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270073368 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 270016780 bp After Masking: 158684050 bp Masked: 41.23 % -- Input Database Coverage: 400181326 bp out of 1417079496 bp ( 28.24 % ) Sampling Time: 00:12:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 07:36:15 (hh:mm:ss) Elapsed Time, 455012 HSPs Collected Number of families returned by RECON: 49592 Round Time: 08:20:08 (hh:mm:ss) Elapsed Time : 996 families discovered. RepeatScout/RECON discovery complete: 2124 families found Classification Time: 00:31:49 (hh:mm:ss) Elapsed Time Program Time: 10:36:19 (hh:mm:ss) Elapsed Time