RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.79kE7P/RM_626611.WedDec40016352024 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: 1733300194 Database = /scratch/tmp/rModeler.79kE7P/GCA_964273585.1_bStrDea1.hap2.1 - Sequences = 584 - Bases = 1200501445 - N50 = 121306202 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 199471513-213719407 | [ 1 ] 185223619-199471512 | [ ] 170975725-185223618 | [ ] 156727831-170975724 | [ 1 ] 142479938-156727831 | [ ] 128232044-142479937 | [ ] 113984150-128232043 | [ 1 ] 99736256-113984149 | [ ] 85488362-99736255 | [ ] 71240469-85488362 | [ 3 ] 56992575-71240468 | [ 2 ] 42744681-56992574 | [ ] 28496787-42744680 | [ ] 14248893-28496786 | [ 8 ] 1000-14248893 |************************************************** [ 568 ] 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 = 40008745 bp ( 40003424 non ambiguous ) - Num Contigs Represented = 86 - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:06 (hh:mm:ss) Elapsed Time Round Time: 00:10:59 (hh:mm:ss) Elapsed Time : 89 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1956 repeats masked totaling 691874 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008966 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10007966 bp After Masking: 8632370 bp Masked: 13.75 % -- Input Database Coverage: 10008966 bp out of 1200501445 bp ( 0.83 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:02 (hh:mm:ss) Elapsed Time, 606 HSPs Collected Number of families returned by RECON: 228 Round Time: 00:03:50 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6041 repeats masked totaling 2052230 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039699 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 30035378 bp After Masking: 26157381 bp Masked: 12.91 % -- Input Database Coverage: 40048665 bp out of 1200501445 bp ( 3.34 % ) Sampling Time: 00:02:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:15:11 (hh:mm:ss) Elapsed Time, 4964 HSPs Collected Number of families returned by RECON: 1352 Round Time: 00:18:30 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18285 repeats masked totaling 5990279 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021646 bp Num Contigs Represented = 151 Non ambiguous bp: Initial: 90009788 bp After Masking: 77777212 bp Masked: 13.59 % -- Input Database Coverage: 130070311 bp out of 1200501445 bp ( 10.83 % ) Sampling Time: 00:05:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 01:38:24 (hh:mm:ss) Elapsed Time, 36748 HSPs Collected Number of families returned by RECON: 7822 Round Time: 01:45:09 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67031 repeats masked totaling 20797723 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270052868 bp Num Contigs Represented = 278 Non ambiguous bp: Initial: 270023505 bp After Masking: 229849737 bp Masked: 14.88 % -- Input Database Coverage: 400123179 bp out of 1200501445 bp ( 33.33 % ) Sampling Time: 00:20:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23232336 Comparison Time: 11:36:28 (hh:mm:ss) Elapsed Time, 225368 HSPs Collected Number of families returned by RECON: 49956 Round Time: 12:10:11 (hh:mm:ss) Elapsed Time : 223 families discovered. RepeatScout/RECON discovery complete: 384 families found Classification Time: 00:13:46 (hh:mm:ss) Elapsed Time Program Time: 14:42:25 (hh:mm:ss) Elapsed Time