RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.1pmcBy/RM_10097.MonJul11425332024 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: 1719869133 Database = /dev/shm/rModeler.1pmcBy/GCA_026437365.1_fEucNew1.0.hap1 - Sequences = 820 - Bases = 984795555 - N50 = 39979434 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 50676705-54295946 | [ 2 ] 47057465-50676705 | [ ] 43438224-47057464 | [ 4 ] 39818984-43438224 | [ 5 ] 36199743-39818983 | [ 5 ] 32580503-36199743 | [ 3 ] 28961262-32580502 | [ 3 ] 25342022-28961262 | [ ] 21722781-25342021 | [ ] 18103541-21722781 | [ ] 14484300-18103540 | [ ] 10865060-14484300 | [ ] 7245819-10865059 | [ ] 3626579-7245819 | [ ] 7339-3626579 |************************************************** [ 798 ] Storage Throughput = excellent ( 1039.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030878 bp ( 40027678 non ambiguous ) - Num Contigs Represented = 123 - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:31:56 (hh:mm:ss) Elapsed Time Round Time: 00:42:24 (hh:mm:ss) Elapsed Time : 511 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10365 repeats masked totaling 1967703 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014163 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10013563 bp After Masking: 5224628 bp Masked: 47.82 % -- Input Database Coverage: 10014163 bp out of 984795555 bp ( 1.02 % ) Sampling Time: 00:10:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:04:36 (hh:mm:ss) Elapsed Time, 8845 HSPs Collected Number of families returned by RECON: 1267 Round Time: 00:15:26 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:34:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33278 repeats masked totaling 6104708 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016707 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 30014107 bp After Masking: 15283350 bp Masked: 49.08 % -- Input Database Coverage: 40030870 bp out of 984795555 bp ( 4.06 % ) Sampling Time: 00:36:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:22:07 (hh:mm:ss) Elapsed Time, 52396 HSPs Collected Number of families returned by RECON: 3858 Round Time: 00:59:34 (hh:mm:ss) Elapsed Time : 113 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:34:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112841 repeats masked totaling 20667337 bp(s). - TE Masking time 00:01:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009787 bp Num Contigs Represented = 208 Non ambiguous bp: Initial: 90002787 bp After Masking: 43738144 bp Masked: 51.40 % -- Input Database Coverage: 130040657 bp out of 984795555 bp ( 13.20 % ) Sampling Time: 01:38:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2611755 Comparison Time: 02:15:31 (hh:mm:ss) Elapsed Time, 209199 HSPs Collected Number of families returned by RECON: 11064 Round Time: 04:02:28 (hh:mm:ss) Elapsed Time : 416 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 04:43:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 395719 repeats masked totaling 72090458 bp(s). - TE Masking time 00:07:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039045 bp Num Contigs Represented = 447 Non ambiguous bp: Initial: 270015916 bp After Masking: 121551905 bp Masked: 54.98 % -- Input Database Coverage: 400079702 bp out of 984795555 bp ( 40.63 % ) Sampling Time: 04:56:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23636250 Comparison Time: 22:27:26 (hh:mm:ss) Elapsed Time, 584479 HSPs Collected Number of families returned by RECON: 33888 Round Time: 28:32:13 (hh:mm:ss) Elapsed Time : 917 families discovered. RepeatScout/RECON discovery complete: 1986 families found Classification Time: 01:12:30 (hh:mm:ss) Elapsed Time Program Time: 35:44:35 (hh:mm:ss) Elapsed Time