RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.kKUfgA/RM_64087.SunNov171421242024 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: 1731882083 Database = /scratch/tmp/rModeler.kKUfgA/GCA_964034855.1_bAnsBra1.1 - Sequences = 715 - Bases = 1287337719 - N50 = 80165619 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198883783-213089697 | [ 1 ] 184677870-198883783 | [ ] 170471957-184677870 | [ ] 156266044-170471957 | [ 1 ] 142060131-156266044 | [ ] 127854218-142060131 | [ ] 113648305-127854218 | [ 1 ] 99442391-113648304 | [ ] 85236478-99442391 | [ ] 71030565-85236478 | [ 2 ] 56824652-71030565 | [ 1 ] 42618739-56824652 | [ 1 ] 28412826-42618739 | [ 3 ] 14206913-28412826 | [ 9 ] 1000-14206913 |************************************************** [ 696 ] Storage Throughput = excellent ( 1416.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008819 bp ( 40002819 non ambiguous ) - Num Contigs Represented = 105 - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:10 (hh:mm:ss) Elapsed Time Round Time: 00:14:28 (hh:mm:ss) Elapsed Time : 64 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 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1539 repeats masked totaling 732161 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003915 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10002915 bp After Masking: 8231521 bp Masked: 17.71 % -- Input Database Coverage: 10003915 bp out of 1287337719 bp ( 0.78 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:51 (hh:mm:ss) Elapsed Time, 410 HSPs Collected Number of families returned by RECON: 227 Round Time: 00:03:53 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5489 repeats masked totaling 2500721 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30044901 bp Num Contigs Represented = 87 Non ambiguous bp: Initial: 30039901 bp After Masking: 25277179 bp Masked: 15.85 % -- Input Database Coverage: 40048816 bp out of 1287337719 bp ( 3.11 % ) Sampling Time: 00:02:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:14:04 (hh:mm:ss) Elapsed Time, 13088 HSPs Collected Number of families returned by RECON: 1179 Round Time: 00:16:41 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18017 repeats masked totaling 7597018 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031744 bp Num Contigs Represented = 185 Non ambiguous bp: Initial: 90017409 bp After Masking: 74329433 bp Masked: 17.43 % -- Input Database Coverage: 130080560 bp out of 1287337719 bp ( 10.10 % ) Sampling Time: 00:08:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 01:28:55 (hh:mm:ss) Elapsed Time, 44610 HSPs Collected Number of families returned by RECON: 7268 Round Time: 01:38:15 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61302 repeats masked totaling 25388015 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270047052 bp Num Contigs Represented = 368 Non ambiguous bp: Initial: 270001252 bp After Masking: 220429992 bp Masked: 18.36 % -- Input Database Coverage: 400127612 bp out of 1287337719 bp ( 31.08 % ) Sampling Time: 00:26:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23355195 Comparison Time: 11:14:25 (hh:mm:ss) Elapsed Time, 216345 HSPs Collected Number of families returned by RECON: 48814 Round Time: 11:54:11 (hh:mm:ss) Elapsed Time : 204 families discovered. RepeatScout/RECON discovery complete: 332 families found Classification Time: 00:14:52 (hh:mm:ss) Elapsed Time Program Time: 14:22:20 (hh:mm:ss) Elapsed Time