RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.CpXSS2/RM_4063319.TueJun101926452025 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: 1749608803 Database = /dev/shm/rModeler.CpXSS2/GCA_000002195.1_Amel_4.5 - Sequences = 5320 - Bases = 250270657 - N50 = 13234341 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 27900550-29893408 | [ 1 ] 25907692-27900549 | [ ] 23914834-25907691 | [ ] 21921976-23914833 | [ ] 19929118-21921975 | [ ] 17936260-19929117 | [ 1 ] 15943402-17936259 | [ ] 13950545-15943402 | [ 3 ] 11957687-13950544 | [ 5 ] 9964829-11957686 | [ 5 ] 7971971-9964828 | [ ] 5979113-7971970 | [ 1 ] 3986255-5979112 | [ ] 1993397-3986254 | [ ] 540-1993397 |************************************************** [ 5304 ] Storage Throughput = excellent ( 1709.61 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43681115 bp ( 40026523 non ambiguous ) - Num Contigs Represented = 1000 - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:34 (hh:mm:ss) Elapsed Time Round Time: 00:10:19 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (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... 697 repeats masked totaling 129665 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11188750 bp Num Contigs Represented = 263 Non ambiguous bp: Initial: 10033920 bp After Masking: 9623963 bp Masked: 4.09 % -- Input Database Coverage: 11188750 bp out of 250270657 bp ( 4.47 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 121278 Comparison Time: 00:16:27 (hh:mm:ss) Elapsed Time, 4009 HSPs Collected Number of families returned by RECON: 917 Round Time: 00:17:21 (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 : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2796 repeats masked totaling 581804 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32522702 bp Num Contigs Represented = 761 Non ambiguous bp: Initial: 30019758 bp After Masking: 28627190 bp Masked: 4.64 % -- Input Database Coverage: 43711452 bp out of 250270657 bp ( 17.47 % ) Sampling Time: 00:01:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1095940 Comparison Time: 01:29:09 (hh:mm:ss) Elapsed Time, 21007 HSPs Collected Number of families returned by RECON: 3872 Round Time: 01:31:43 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8905 repeats masked totaling 1906996 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 97611829 bp Num Contigs Represented = 2101 Non ambiguous bp: Initial: 90025696 bp After Masking: 85579865 bp Masked: 4.94 % -- Input Database Coverage: 141323281 bp out of 250270657 bp ( 56.47 % ) Sampling Time: 00:05:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 9251451 Comparison Time: 10:27:17 (hh:mm:ss) Elapsed Time, 153694 HSPs Collected Number of families returned by RECON: 18996 Round Time: 10:40:07 (hh:mm:ss) Elapsed Time : 83 families discovered. - Increasing sample size to include end piece now = 386559205 RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15799 repeats masked totaling 3841795 bp(s). - TE Masking time 00:04:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 108947024 bp Num Contigs Represented = 2402 Non ambiguous bp: Initial: 99025832 bp After Masking: 92470497 bp Masked: 6.62 % -- Input Database Coverage: 250270305 bp out of 250270657 bp ( 100.00 % ) Sampling Time: 00:09:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 11934055 Comparison Time: 12:06:05 (hh:mm:ss) Elapsed Time, 87606 HSPs Collected Number of families returned by RECON: 19294 Round Time: 12:18:56 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatScout/RECON discovery complete: 227 families found Classification Time: 00:09:51 (hh:mm:ss) Elapsed Time Program Time: 25:08:17 (hh:mm:ss) Elapsed Time