RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.pG2EAC/RM_1749781.SunJul210556342024 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: 1721566594 Database = /dev/shm/rModeler.pG2EAC/GCF_023373465.1_Oket_V2 - Sequences = 14075 - Bases = 2556477726 - N50 = 54879299 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 94062740-100781491 | [ 1 ] 87343989-94062739 | [ 2 ] 80625238-87343988 | [ 5 ] 73906487-80625237 | [ 1 ] 67187737-73906487 | [ ] 60468986-67187736 | [ 2 ] 53750235-60468985 | [ 6 ] 47031484-53750234 | [ 9 ] 40312733-47031483 | [ 3 ] 33593983-40312733 | [ 3 ] 26875232-33593982 | [ 3 ] 20156481-26875231 | [ 2 ] 13437730-20156480 | [ ] 6718979-13437729 | [ ] 229-6718979 |************************************************** [ 14038 ] Storage Throughput = good ( 809.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014593 bp ( 40010393 non ambiguous ) - Num Contigs Represented = 378 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:24 (hh:mm:ss) Elapsed Time Round Time: 00:23:20 (hh:mm:ss) Elapsed Time : 760 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12232 repeats masked totaling 3100440 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039766 bp Num Contigs Represented = 129 Non ambiguous bp: Initial: 10038966 bp After Masking: 3988636 bp Masked: 60.27 % -- Input Database Coverage: 10039766 bp out of 2556477726 bp ( 0.39 % ) Sampling Time: 00:08:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 43956 Comparison Time: 00:04:34 (hh:mm:ss) Elapsed Time, 7450 HSPs Collected Number of families returned by RECON: 1073 Round Time: 00:12:47 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37270 repeats masked totaling 9543718 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014766 bp Num Contigs Represented = 286 Non ambiguous bp: Initial: 30011366 bp After Masking: 11265083 bp Masked: 62.46 % -- Input Database Coverage: 40054532 bp out of 2556477726 bp ( 1.57 % ) Sampling Time: 00:25:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 371091 Comparison Time: 00:22:23 (hh:mm:ss) Elapsed Time, 36546 HSPs Collected Number of families returned by RECON: 3317 Round Time: 00:49:12 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:11:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 119024 repeats masked totaling 29726991 bp(s). - TE Masking time 00:01:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018355 bp Num Contigs Represented = 763 Non ambiguous bp: Initial: 90008386 bp After Masking: 33250738 bp Masked: 63.06 % -- Input Database Coverage: 130072887 bp out of 2556477726 bp ( 5.09 % ) Sampling Time: 01:15:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3381300 Comparison Time: 02:28:19 (hh:mm:ss) Elapsed Time, 218019 HSPs Collected Number of families returned by RECON: 9417 Round Time: 03:53:11 (hh:mm:ss) Elapsed Time : 433 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 04:12:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 400159 repeats masked totaling 99264725 bp(s). - TE Masking time 00:07:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044274 bp Num Contigs Represented = 2282 Non ambiguous bp: Initial: 270007413 bp After Masking: 87514375 bp Masked: 67.59 % -- Input Database Coverage: 400117161 bp out of 2556477726 bp ( 15.65 % ) Sampling Time: 04:29:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31692741 Comparison Time: 19:34:17 (hh:mm:ss) Elapsed Time, 525356 HSPs Collected Number of families returned by RECON: 30716 Round Time: 25:01:28 (hh:mm:ss) Elapsed Time : 863 families discovered. RepeatScout/RECON discovery complete: 2162 families found Classification Time: 01:13:09 (hh:mm:ss) Elapsed Time Program Time: 31:33:08 (hh:mm:ss) Elapsed Time