RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.2KlpP6/RM_2012657.MonDec21736222024 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: 1733189782 Database = /scratch/tmp/rModeler.2KlpP6/GCF_040869285.1_UKY_Mglu_1.0 - Sequences = 4270 - Bases = 3829277745 - N50 = 174632329 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 378676600-405724300 | [ 1 ] 351628901-378676600 | [ ] 324581202-351628901 | [ ] 297533503-324581202 | [ ] 270485804-297533503 | [ 1 ] 243438104-270485803 | [ ] 216390405-243438104 | [ 2 ] 189342706-216390405 | [ 3 ] 162295007-189342706 | [ 1 ] 135247308-162295007 | [ 3 ] 108199608-135247307 | [ 3 ] 81151909-108199608 | [ 1 ] 54104210-81151909 | [ ] 27056511-54104210 | [ 1 ] 8812-27056511 |************************************************** [ 4254 ] Storage Throughput = excellent ( 1425.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036864 bp ( 40019930 non ambiguous ) - Num Contigs Represented = 263 - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:59 (hh:mm:ss) Elapsed Time Round Time: 00:26:31 (hh:mm:ss) Elapsed Time : 739 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13255 repeats masked totaling 5256862 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10043638 bp Num Contigs Represented = 85 Non ambiguous bp: Initial: 10039538 bp After Masking: 2027510 bp Masked: 79.80 % -- Input Database Coverage: 10043638 bp out of 3829277745 bp ( 0.26 % ) Sampling Time: 00:03:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:02:50 (hh:mm:ss) Elapsed Time, 4857 HSPs Collected Number of families returned by RECON: 753 Round Time: 00:06:07 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40669 repeats masked totaling 15809108 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033226 bp Num Contigs Represented = 205 Non ambiguous bp: Initial: 30020392 bp After Masking: 6401065 bp Masked: 78.68 % -- Input Database Coverage: 40076864 bp out of 3829277745 bp ( 1.05 % ) Sampling Time: 00:10:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:09:50 (hh:mm:ss) Elapsed Time, 28933 HSPs Collected Number of families returned by RECON: 2487 Round Time: 00:20:16 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 124742 repeats masked totaling 46963003 bp(s). - TE Masking time 00:01:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90079041 bp Num Contigs Represented = 556 Non ambiguous bp: Initial: 90035306 bp After Masking: 18394851 bp Masked: 79.57 % -- Input Database Coverage: 130155905 bp out of 3829277745 bp ( 3.40 % ) Sampling Time: 00:32:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 00:40:54 (hh:mm:ss) Elapsed Time, 229279 HSPs Collected Number of families returned by RECON: 6497 Round Time: 01:15:33 (hh:mm:ss) Elapsed Time : 338 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:12:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 420908 repeats masked totaling 153299135 bp(s). - TE Masking time 00:04:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270193047 bp Num Contigs Represented = 1220 Non ambiguous bp: Initial: 270035468 bp After Masking: 47475848 bp Masked: 82.42 % -- Input Database Coverage: 400348952 bp out of 3829277745 bp ( 10.45 % ) Sampling Time: 01:28:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23836060 Comparison Time: 03:38:05 (hh:mm:ss) Elapsed Time, 651175 HSPs Collected Number of families returned by RECON: 15469 Round Time: 05:17:47 (hh:mm:ss) Elapsed Time : 918 families discovered. RepeatScout/RECON discovery complete: 2054 families found Classification Time: 00:56:22 (hh:mm:ss) Elapsed Time Program Time: 08:22:36 (hh:mm:ss) Elapsed Time