RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.hgFI4C/RM_2387226.ThuJul111548592024 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: 1720738139 Database = /dev/shm/rModeler.hgFI4C/GCF_027744825.2_RoL_Sspl_1.0 - Sequences = 97 - Bases = 582898256 Storage Throughput = excellent ( 1404.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001591 bp ( 40001591 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:03 (hh:mm:ss) Elapsed Time Round Time: 00:21:07 (hh:mm:ss) Elapsed Time : 328 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (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... 5993 repeats masked totaling 1146671 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027979 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10027979 bp After Masking: 7391216 bp Masked: 26.29 % -- Input Database Coverage: 10027979 bp out of 582898256 bp ( 1.72 % ) Sampling Time: 00:01:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:03 (hh:mm:ss) Elapsed Time, 6395 HSPs Collected Number of families returned by RECON: 1042 Round Time: 00:07:25 (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 : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16945 repeats masked totaling 2949362 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013532 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30013532 bp After Masking: 23310891 bp Masked: 22.33 % -- Input Database Coverage: 40041511 bp out of 582898256 bp ( 6.87 % ) Sampling Time: 00:03:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:29:23 (hh:mm:ss) Elapsed Time, 39960 HSPs Collected Number of families returned by RECON: 4232 Round Time: 00:33:53 (hh:mm:ss) Elapsed Time : 99 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62442 repeats masked totaling 11950550 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90005196 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 90005136 bp After Masking: 64957365 bp Masked: 27.83 % -- Input Database Coverage: 130046707 bp out of 582898256 bp ( 22.31 % ) Sampling Time: 00:10:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 02:44:23 (hh:mm:ss) Elapsed Time, 176466 HSPs Collected Number of families returned by RECON: 13037 Round Time: 03:04:42 (hh:mm:ss) Elapsed Time : 274 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 229937 repeats masked totaling 43361233 bp(s). - TE Masking time 00:05:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270002032 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 270001851 bp After Masking: 187870122 bp Masked: 30.42 % -- Input Database Coverage: 400048739 bp out of 582898256 bp ( 68.63 % ) Sampling Time: 00:32:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22926606 Comparison Time: 18:57:25 (hh:mm:ss) Elapsed Time, 478029 HSPs Collected Number of families returned by RECON: 53139 Round Time: 20:17:24 (hh:mm:ss) Elapsed Time : 659 families discovered. RepeatScout/RECON discovery complete: 1368 families found Classification Time: 01:06:49 (hh:mm:ss) Elapsed Time Program Time: 25:31:20 (hh:mm:ss) Elapsed Time