RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zAUxbD/RM_3674136.SatNov252137302023 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: 1700977049 Database = /dev/shm/rModeler.zAUxbD/GCF_958295425.1_fSolSol10.1 - Sequences = 242 - Bases = 643757955 - N50 = 29764166 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 43927365-47064963 | [ 1 ] 40789767-43927364 | [ ] 37652170-40789767 | [ 1 ] 34514572-37652169 | [ 1 ] 31376975-34514572 | [ 3 ] 28239377-31376974 |* [ 6 ] 25101780-28239377 |* [ 5 ] 21964182-25101779 | [ 4 ] 18826585-21964182 | [ ] 15688987-18826584 | [ ] 12551390-15688987 | [ ] 9413792-12551389 | [ ] 6276195-9413792 | [ ] 3138597-6276194 | [ ] 1000-3138597 |************************************************** [ 221 ] Storage Throughput = excellent ( 1474.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023625 bp ( 40019225 non ambiguous ) - Num Contigs Represented = 59 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:18 (hh:mm:ss) Elapsed Time Round Time: 00:22:58 (hh:mm:ss) Elapsed Time : 428 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9503 repeats masked totaling 1157857 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006192 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10005392 bp After Masking: 8234357 bp Masked: 17.70 % -- Input Database Coverage: 10006192 bp out of 643757955 bp ( 1.55 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:08:48 (hh:mm:ss) Elapsed Time, 13330 HSPs Collected Number of families returned by RECON: 1895 Round Time: 00:11:22 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30460 repeats masked totaling 3906255 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017353 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30013753 bp After Masking: 23604389 bp Masked: 21.35 % -- Input Database Coverage: 40023545 bp out of 643757955 bp ( 6.22 % ) Sampling Time: 00:04:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:34:09 (hh:mm:ss) Elapsed Time, 116842 HSPs Collected Number of families returned by RECON: 6815 Round Time: 00:40:38 (hh:mm:ss) Elapsed Time : 134 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 110406 repeats masked totaling 14681738 bp(s). - TE Masking time 00:01:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020128 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 90006862 bp After Masking: 68995802 bp Masked: 23.34 % -- Input Database Coverage: 130043673 bp out of 643757955 bp ( 20.20 % ) Sampling Time: 00:13:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 03:35:35 (hh:mm:ss) Elapsed Time, 705794 HSPs Collected Number of families returned by RECON: 23165 Round Time: 04:05:53 (hh:mm:ss) Elapsed Time : 474 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 402963 repeats masked totaling 55516839 bp(s). - TE Masking time 00:08:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039463 bp Num Contigs Represented = 143 Non ambiguous bp: Initial: 270012463 bp After Masking: 195351765 bp Masked: 27.65 % -- Input Database Coverage: 400083136 bp out of 643757955 bp ( 62.15 % ) Sampling Time: 00:42:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23096206 Comparison Time: 27:07:32 (hh:mm:ss) Elapsed Time, 2955175 HSPs Collected Number of families returned by RECON: 85586 Round Time: 30:04:39 (hh:mm:ss) Elapsed Time : 1164 families discovered. RepeatScout/RECON discovery complete: 2230 families found Classification Time: 01:20:54 (hh:mm:ss) Elapsed Time Program Time: 36:46:24 (hh:mm:ss) Elapsed Time