RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.mHGf9V/RM_3814743.TueDec30948292024 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: 1733248108 Database = /scratch/tmp/rModeler.mHGf9V/GCF_027789765.1_aDenEbr1.pat - Sequences = 2200 - Bases = 2214937069 - N50 = 163017972 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 218804114-234432908 | [ 2 ] 203175320-218804113 | [ ] 187546527-203175320 | [ 1 ] 171917733-187546526 | [ 1 ] 156288940-171917733 | [ 1 ] 140660146-156288939 | [ 2 ] 125031353-140660146 | [ 1 ] 109402559-125031352 | [ 1 ] 93773766-109402559 | [ 2 ] 78144972-93773765 | [ 3 ] 62516179-78144972 | [ 1 ] 46887385-62516178 | [ ] 31258592-46887385 | [ ] 15629798-31258591 | [ ] 1005-15629798 |************************************************** [ 2185 ] Storage Throughput = excellent ( 1472.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40047501 bp ( 40030314 non ambiguous ) - Num Contigs Represented = 87 - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:05:59 (hh:mm:ss) Elapsed Time Round Time: 00:12:20 (hh:mm:ss) Elapsed Time : 918 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20421 repeats masked totaling 4005731 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006426 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10005813 bp After Masking: 4642185 bp Masked: 53.61 % -- Input Database Coverage: 10006426 bp out of 2214937069 bp ( 0.45 % ) Sampling Time: 00:01:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:02:53 (hh:mm:ss) Elapsed Time, 14356 HSPs Collected Number of families returned by RECON: 1456 Round Time: 00:04:49 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62460 repeats masked totaling 11900625 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040995 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 30024421 bp After Masking: 13632986 bp Masked: 54.59 % -- Input Database Coverage: 40047421 bp out of 2214937069 bp ( 1.81 % ) Sampling Time: 00:05:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:12:50 (hh:mm:ss) Elapsed Time, 81585 HSPs Collected Number of families returned by RECON: 4631 Round Time: 00:19:36 (hh:mm:ss) Elapsed Time : 146 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 194083 repeats masked totaling 36823599 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90335645 bp Num Contigs Represented = 201 Non ambiguous bp: Initial: 90036237 bp After Masking: 39078746 bp Masked: 56.60 % -- Input Database Coverage: 130383066 bp out of 2214937069 bp ( 5.89 % ) Sampling Time: 00:19:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2683086 Comparison Time: 01:16:11 (hh:mm:ss) Elapsed Time, 551329 HSPs Collected Number of families returned by RECON: 12777 Round Time: 01:40:34 (hh:mm:ss) Elapsed Time : 514 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:44:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 668975 repeats masked totaling 126184634 bp(s). - TE Masking time 00:04:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270773518 bp Num Contigs Represented = 479 Non ambiguous bp: Initial: 270038301 bp After Masking: 104099153 bp Masked: 61.45 % -- Input Database Coverage: 401156584 bp out of 2214937069 bp ( 18.11 % ) Sampling Time: 00:59:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23925903 Comparison Time: 07:06:47 (hh:mm:ss) Elapsed Time, 2067226 HSPs Collected Number of families returned by RECON: 35491 Round Time: 08:31:06 (hh:mm:ss) Elapsed Time : 1294 families discovered. RepeatScout/RECON discovery complete: 2898 families found Classification Time: 00:43:48 (hh:mm:ss) Elapsed Time Program Time: 11:32:13 (hh:mm:ss) Elapsed Time