RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.LTyK5B/RM_10933.SatNov160532022024 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: 1731763920 Database = /scratch/tmp/rModeler.LTyK5B/GCA_964234715.1_rPodMel1.hap1.1 - Sequences = 386 - Bases = 1574923724 - N50 = 99258882 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 127639102-136756110 | [ 1 ] 118522095-127639102 | [ 2 ] 109405088-118522095 | [ ] 100288080-109405087 | [ 2 ] 91171073-100288080 | [ 2 ] 82054066-91171073 | [ 1 ] 72937058-82054065 | [ 2 ] 63820051-72937058 | [ ] 54703044-63820051 | [ 3 ] 45586036-54703043 | [ 2 ] 36469029-45586036 | [ 4 ] 27352022-36469029 | [ ] 18235014-27352021 | [ ] 9118007-18235014 | [ 1 ] 1000-9118007 |************************************************** [ 366 ] Storage Throughput = fair ( 625.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003980 bp ( 40000580 non ambiguous ) - Num Contigs Represented = 58 - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:50 (hh:mm:ss) Elapsed Time Round Time: 00:29:51 (hh:mm:ss) Elapsed Time : 531 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17782 repeats masked totaling 2995317 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014771 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10013771 bp After Masking: 6345584 bp Masked: 36.63 % -- Input Database Coverage: 10014771 bp out of 1574923724 bp ( 0.64 % ) Sampling Time: 00:02:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:50 (hh:mm:ss) Elapsed Time, 8304 HSPs Collected Number of families returned by RECON: 1302 Round Time: 00:07:52 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52149 repeats masked totaling 9456801 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029056 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30026656 bp After Masking: 18095031 bp Masked: 39.74 % -- Input Database Coverage: 40043827 bp out of 1574923724 bp ( 2.54 % ) Sampling Time: 00:09:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:24:25 (hh:mm:ss) Elapsed Time, 47534 HSPs Collected Number of families returned by RECON: 4074 Round Time: 00:35:42 (hh:mm:ss) Elapsed Time : 121 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 174706 repeats masked totaling 30338708 bp(s). - TE Masking time 00:01:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037202 bp Num Contigs Represented = 111 Non ambiguous bp: Initial: 90029402 bp After Masking: 52994637 bp Masked: 41.14 % -- Input Database Coverage: 130081029 bp out of 1574923724 bp ( 8.26 % ) Sampling Time: 00:28:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 02:46:38 (hh:mm:ss) Elapsed Time, 191646 HSPs Collected Number of families returned by RECON: 13348 Round Time: 03:28:07 (hh:mm:ss) Elapsed Time : 413 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 594424 repeats masked totaling 102174580 bp(s). - TE Masking time 00:08:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039656 bp Num Contigs Represented = 210 Non ambiguous bp: Initial: 270006991 bp After Masking: 148176302 bp Masked: 45.12 % -- Input Database Coverage: 400120685 bp out of 1574923724 bp ( 25.41 % ) Sampling Time: 01:22:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 21:04:50 (hh:mm:ss) Elapsed Time, 502899 HSPs Collected Number of families returned by RECON: 45705 Round Time: 24:05:36 (hh:mm:ss) Elapsed Time : 1061 families discovered. RepeatScout/RECON discovery complete: 2143 families found Classification Time: 01:10:30 (hh:mm:ss) Elapsed Time Program Time: 29:57:38 (hh:mm:ss) Elapsed Time