RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ZO4J3S/RM_359043.MonJun241444162024 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: 1719265452 Database = /dev/shm/rModeler.ZO4J3S/GCF_963691925.1_fScoSco1.1 - Sequences = 665 - Bases = 764141294 - N50 = 31899851 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 36171244-38754833 | [ 2 ] 33587655-36171243 | [ 4 ] 31004066-33587654 | [ 6 ] 28420477-31004065 | [ 7 ] 25836888-28420476 | [ ] 23253299-25836887 | [ 4 ] 20669710-23253298 | [ ] 18086122-20669710 | [ ] 15502533-18086121 | [ 1 ] 12918944-15502532 | [ ] 10335355-12918943 | [ ] 7751766-10335354 | [ ] 5168177-7751765 | [ ] 2584588-5168176 | [ ] 1000-2584588 |************************************************** [ 641 ] Storage Throughput = excellent ( 1277.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40055209 bp ( 40038809 non ambiguous ) - Num Contigs Represented = 86 - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:34 (hh:mm:ss) Elapsed Time Round Time: 00:16:48 (hh:mm:ss) Elapsed Time : 418 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6388 repeats masked totaling 872619 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024153 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 10019953 bp After Masking: 8272549 bp Masked: 17.44 % -- Input Database Coverage: 10024153 bp out of 764141294 bp ( 1.31 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33670 Comparison Time: 00:06:36 (hh:mm:ss) Elapsed Time, 9730 HSPs Collected Number of families returned by RECON: 1572 Round Time: 00:08:17 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21596 repeats masked totaling 2984579 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030976 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 30018776 bp After Masking: 24727897 bp Masked: 17.63 % -- Input Database Coverage: 40055129 bp out of 764141294 bp ( 5.24 % ) Sampling Time: 00:03:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:28:55 (hh:mm:ss) Elapsed Time, 50303 HSPs Collected Number of families returned by RECON: 6074 Round Time: 00:33:26 (hh:mm:ss) Elapsed Time : 122 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77441 repeats masked totaling 10892751 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90066479 bp Num Contigs Represented = 147 Non ambiguous bp: Initial: 90033835 bp After Masking: 72489092 bp Masked: 19.49 % -- Input Database Coverage: 130121608 bp out of 764141294 bp ( 17.03 % ) Sampling Time: 00:10:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2636956 Comparison Time: 02:40:32 (hh:mm:ss) Elapsed Time, 290243 HSPs Collected Number of families returned by RECON: 21406 Round Time: 03:01:22 (hh:mm:ss) Elapsed Time : 509 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 304187 repeats masked totaling 45951873 bp(s). - TE Masking time 00:04:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270138711 bp Num Contigs Represented = 300 Non ambiguous bp: Initial: 270033245 bp After Masking: 203828500 bp Masked: 24.52 % -- Input Database Coverage: 400260319 bp out of 764141294 bp ( 52.38 % ) Sampling Time: 00:33:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23615628 Comparison Time: 17:14:29 (hh:mm:ss) Elapsed Time, 1006192 HSPs Collected Number of families returned by RECON: 75118 Round Time: 19:48:18 (hh:mm:ss) Elapsed Time : 1433 families discovered. RepeatScout/RECON discovery complete: 2498 families found Classification Time: 01:10:25 (hh:mm:ss) Elapsed Time Program Time: 24:58:36 (hh:mm:ss) Elapsed Time