RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.YOvlyz/RM_31066.SatNov252139332023 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: 1700977150 Database = /dev/shm/rModeler.YOvlyz/GCA_011762535.1_mTurTru1.mat - Sequences = 985 - Bases = 2385753970 - N50 = 95202452 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 149280894-159943777 | [ 2 ] 138618011-149280893 | [ ] 127955128-138618010 | [ ] 117292245-127955127 | [ 1 ] 106629362-117292244 | [ 2 ] 95966479-106629361 | [ 4 ] 85303596-95966478 | [ 5 ] 74640714-85303596 | [ 3 ] 63977831-74640713 | [ ] 53314948-63977830 | [ 3 ] 42652065-53314947 | [ 1 ] 31989182-42652064 | [ 4 ] 21326299-31989181 | [ 6 ] 10663416-21326298 | [ 3 ] 534-10663416 |************************************************** [ 951 ] Storage Throughput = excellent ( 1175.22 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40244465 bp ( 40031004 non ambiguous ) - Num Contigs Represented = 73 - Sequence extraction : 00:01:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:52 (hh:mm:ss) Elapsed Time Round Time: 00:33:31 (hh:mm:ss) Elapsed Time : 216 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (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... 8956 repeats masked totaling 2574063 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10042497 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10033097 bp After Masking: 7404264 bp Masked: 26.20 % -- Input Database Coverage: 10042497 bp out of 2385753970 bp ( 0.42 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:05:52 (hh:mm:ss) Elapsed Time, 12170 HSPs Collected Number of families returned by RECON: 1087 Round Time: 00:07:27 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:25 (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... 32504 repeats masked totaling 9467455 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30241959 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 30037898 bp After Masking: 20434831 bp Masked: 31.97 % -- Input Database Coverage: 40284456 bp out of 2385753970 bp ( 1.69 % ) Sampling Time: 00:03:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:30:53 (hh:mm:ss) Elapsed Time, 25572 HSPs Collected Number of families returned by RECON: 2644 Round Time: 00:35:03 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111965 repeats masked totaling 30486434 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90227247 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 90033602 bp After Masking: 59131222 bp Masked: 34.32 % -- Input Database Coverage: 130511703 bp out of 2385753970 bp ( 5.47 % ) Sampling Time: 00:16:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 04:07:49 (hh:mm:ss) Elapsed Time, 80038 HSPs Collected Number of families returned by RECON: 8718 Round Time: 04:29:10 (hh:mm:ss) Elapsed Time : 157 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 366235 repeats masked totaling 97775211 bp(s). - TE Masking time 00:05:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270740570 bp Num Contigs Represented = 227 Non ambiguous bp: Initial: 270026671 bp After Masking: 170754051 bp Masked: 36.76 % -- Input Database Coverage: 401252273 bp out of 2385753970 bp ( 16.82 % ) Sampling Time: 00:36:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23423590 Comparison Time: 26:59:43 (hh:mm:ss) Elapsed Time, 268770 HSPs Collected Number of families returned by RECON: 36536 Round Time: 28:06:48 (hh:mm:ss) Elapsed Time : 354 families discovered. RepeatScout/RECON discovery complete: 827 families found Classification Time: 00:29:36 (hh:mm:ss) Elapsed Time Program Time: 34:21:35 (hh:mm:ss) Elapsed Time