RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.Tq604E/RM_3896896.SunJul201631112025 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: 1753054270 Database = /data/tmp/rModeler.Tq604E/GCA_965202575.1_ktThaDemo2.hap2.1 - Sequences = 1217 - Bases = 790658053 - N50 = 100745342 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 123517653-132340272 | [ 1 ] 114695035-123517653 | [ ] 105872417-114695035 | [ ] 97049799-105872417 | [ 2 ] 88227181-97049799 | [ ] 79404563-88227181 | [ 2 ] 70581945-79404563 | [ 1 ] 61759326-70581944 | [ ] 52936708-61759326 | [ 2 ] 44114090-52936708 | [ ] 35291472-44114090 | [ 1 ] 26468854-35291472 | [ ] 17646236-26468854 | [ ] 8823618-17646236 | [ ] 1000-8823618 |************************************************** [ 1208 ] Storage Throughput = excellent ( 1203.58 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012710 bp ( 40011610 non ambiguous ) - Num Contigs Represented = 106 - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:59 (hh:mm:ss) Elapsed Time Round Time: 00:41:07 (hh:mm:ss) Elapsed Time : 469 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9557 repeats masked totaling 2526708 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010762 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10010562 bp After Masking: 6980209 bp Masked: 30.27 % -- Input Database Coverage: 10010762 bp out of 790658053 bp ( 1.27 % ) Sampling Time: 00:02:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:14:19 (hh:mm:ss) Elapsed Time, 3665 HSPs Collected Number of families returned by RECON: 674 Round Time: 00:17:34 (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 : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29945 repeats masked totaling 7847082 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001868 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 30000968 bp After Masking: 20769409 bp Masked: 30.77 % -- Input Database Coverage: 40012630 bp out of 790658053 bp ( 5.06 % ) Sampling Time: 00:07:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 301476 Comparison Time: 01:20:23 (hh:mm:ss) Elapsed Time, 70503 HSPs Collected Number of families returned by RECON: 2897 Round Time: 01:30:52 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 95319 repeats masked totaling 25116799 bp(s). - TE Masking time 00:07:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034913 bp Num Contigs Represented = 233 Non ambiguous bp: Initial: 90028880 bp After Masking: 61528127 bp Masked: 31.66 % -- Input Database Coverage: 130047543 bp out of 790658053 bp ( 16.45 % ) Sampling Time: 00:21:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2680770 Comparison Time: 09:24:10 (hh:mm:ss) Elapsed Time, 301999 HSPs Collected Number of families returned by RECON: 10173 Round Time: 10:21:12 (hh:mm:ss) Elapsed Time : 242 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 322128 repeats masked totaling 89503235 bp(s). - TE Masking time 00:40:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032914 bp Num Contigs Represented = 567 Non ambiguous bp: Initial: 270017747 bp After Masking: 170286795 bp Masked: 36.93 % -- Input Database Coverage: 400080457 bp out of 790658053 bp ( 50.60 % ) Sampling Time: 01:30:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24106096 Comparison Time: 66:04:09 (hh:mm:ss) Elapsed Time, 1124563 HSPs Collected Number of families returned by RECON: 31763 Round Time: 69:17:31 (hh:mm:ss) Elapsed Time : 609 families discovered. RepeatScout/RECON discovery complete: 1370 families found Classification Time: 02:22:44 (hh:mm:ss) Elapsed Time Program Time: 84:31:00 (hh:mm:ss) Elapsed Time