RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.awA8O9/RM_1336173.TueApr222150522025 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: 1745383852 Database = /data/tmp/rModeler.awA8O9/GCA_964204655.1_aTriCri1.1 - Sequences = 435 - Bases = 8051561466 - N50 = 1361375652 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1820627706-1950672471 | [ 1 ] 1690582941-1820627705 | [ ] 1560538176-1690582940 | [ ] 1430493412-1560538176 | [ ] 1300448647-1430493411 | [ 1 ] 1170403882-1300448646 | [ 3 ] 1040359117-1170403881 | [ ] 910314353-1040359117 | [ 1 ] 780269588-910314352 | [ ] 650224823-780269587 | [ ] 520180058-650224822 | [ ] 390135294-520180058 | [ ] 260090529-390135293 | [ ] 130045764-260090528 | [ ] 1000-130045764 |************************************************** [ 429 ] Storage Throughput = excellent ( 1124.12 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011086 bp ( 40010086 non ambiguous ) - Num Contigs Represented = 15 - Sequence extraction : 00:32:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:48 (hh:mm:ss) Elapsed Time Round Time: 01:08:26 (hh:mm:ss) Elapsed Time : 700 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:07:23 (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... 10983 repeats masked totaling 4401068 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015374 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 10015374 bp After Masking: 5035018 bp Masked: 49.73 % -- Input Database Coverage: 10015374 bp out of 8051561466 bp ( 0.12 % ) Sampling Time: 00:08:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:40 (hh:mm:ss) Elapsed Time, 22067 HSPs Collected Number of families returned by RECON: 1268 Round Time: 00:16:05 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:22:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34361 repeats masked totaling 13605354 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035632 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 30034632 bp After Masking: 14129083 bp Masked: 52.96 % -- Input Database Coverage: 40051006 bp out of 8051561466 bp ( 0.50 % ) Sampling Time: 00:26:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:22:57 (hh:mm:ss) Elapsed Time, 66612 HSPs Collected Number of families returned by RECON: 4148 Round Time: 00:55:50 (hh:mm:ss) Elapsed Time : 87 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 01:05:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 106940 repeats masked totaling 43080773 bp(s). - TE Masking time 00:02:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037262 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 90032662 bp After Masking: 39772223 bp Masked: 55.82 % -- Input Database Coverage: 130088268 bp out of 8051561466 bp ( 1.62 % ) Sampling Time: 01:21:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:00:31 (hh:mm:ss) Elapsed Time, 376575 HSPs Collected Number of families returned by RECON: 12030 Round Time: 03:53:25 (hh:mm:ss) Elapsed Time : 406 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 03:41:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 373352 repeats masked totaling 148594678 bp(s). - TE Masking time 00:12:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028212 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 270017468 bp After Masking: 100029504 bp Masked: 62.95 % -- Input Database Coverage: 400116480 bp out of 8051561466 bp ( 4.97 % ) Sampling Time: 04:31:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 11:49:13 (hh:mm:ss) Elapsed Time, 1573308 HSPs Collected Number of families returned by RECON: 32919 Round Time: 19:07:58 (hh:mm:ss) Elapsed Time : 1088 families discovered. RepeatScout/RECON discovery complete: 2293 families found Classification Time: 01:55:19 (hh:mm:ss) Elapsed Time Program Time: 27:17:03 (hh:mm:ss) Elapsed Time