RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VhLgWj/RM_102414.FriJan131724152023 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: 1673659454 Database = /dev/shm/rModeler.VhLgWj/GCA_903684865.1_fDreABH1.1 - Sequences = 1252 - Bases = 1354075779 - N50 = 54645068 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 69471728-74433922 | [ 1 ] 64509535-69471728 | [ ] 59547341-64509534 | [ 3 ] 54585148-59547341 | [ 7 ] 49622955-54585148 | [ 6 ] 44660761-49622954 | [ 4 ] 39698568-44660761 | [ 1 ] 34736374-39698567 | [ 2 ] 29774181-34736374 | [ 1 ] 24811988-29774181 | [ ] 19849794-24811987 | [ ] 14887601-19849794 | [ ] 9925407-14887600 | [ ] 4963214-9925407 | [ ] 1021-4963214 |************************************************** [ 1227 ] Storage Throughput = excellent ( 1211.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019928 bp ( 40018203 non ambiguous ) - Num Contigs Represented = 87 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:37 (hh:mm:ss) Elapsed Time Round Time: 00:26:28 (hh:mm:ss) Elapsed Time : 1058 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22204 repeats masked totaling 4205432 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002214 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10001989 bp After Masking: 5231863 bp Masked: 47.69 % -- Input Database Coverage: 10002214 bp out of 1354075779 bp ( 0.74 % ) Sampling Time: 00:02:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:06:26 (hh:mm:ss) Elapsed Time, 10770 HSPs Collected Number of families returned by RECON: 1282 Round Time: 00:09:33 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65793 repeats masked totaling 12690170 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017634 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30016134 bp After Masking: 15630738 bp Masked: 47.93 % -- Input Database Coverage: 40019848 bp out of 1354075779 bp ( 2.96 % ) Sampling Time: 00:06:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:28:40 (hh:mm:ss) Elapsed Time, 56440 HSPs Collected Number of families returned by RECON: 4335 Round Time: 00:36:52 (hh:mm:ss) Elapsed Time : 132 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 207228 repeats masked totaling 40060848 bp(s). - TE Masking time 00:03:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90061367 bp Num Contigs Represented = 134 Non ambiguous bp: Initial: 90017246 bp After Masking: 45107784 bp Masked: 49.89 % -- Input Database Coverage: 130081215 bp out of 1354075779 bp ( 9.61 % ) Sampling Time: 00:18:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2607186 Comparison Time: 02:59:01 (hh:mm:ss) Elapsed Time, 318460 HSPs Collected Number of families returned by RECON: 11715 Round Time: 03:31:38 (hh:mm:ss) Elapsed Time : 630 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 710804 repeats masked totaling 137228824 bp(s). - TE Masking time 00:22:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028138 bp Num Contigs Represented = 388 Non ambiguous bp: Initial: 270018093 bp After Masking: 117255710 bp Masked: 56.57 % -- Input Database Coverage: 400109353 bp out of 1354075779 bp ( 29.55 % ) Sampling Time: 01:15:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23739495 Comparison Time: 18:30:25 (hh:mm:ss) Elapsed Time, 724493 HSPs Collected Number of families returned by RECON: 31104 Round Time: 20:36:07 (hh:mm:ss) Elapsed Time : 1248 families discovered. RepeatScout/RECON discovery complete: 3089 families found Classification Time: 02:09:23 (hh:mm:ss) Elapsed Time Program Time: 27:30:01 (hh:mm:ss) Elapsed Time