RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.lABExZ/RM_30453.MonJul10716282024 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: 1719843387 Database = /dev/shm/rModeler.lABExZ/GCA_024217435.4_RoL_Ssco_1.2 - Sequences = 496 - Bases = 428417373 - N50 = 17757856 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 28093364-30098933 | [ 2 ] 26087795-28093363 | [ ] 24082227-26087795 | [ 2 ] 22076658-24082226 | [ ] 20071090-22076658 | [ 3 ] 18065521-20071089 | [ 1 ] 16059952-18065520 | [ 3 ] 14054384-16059952 | [ 4 ] 12048815-14054383 | [ 5 ] 10043247-12048815 | [ 1 ] 8037678-10043246 | [ ] 6032109-8037677 | [ 1 ] 4026541-6032109 | [ ] 2020972-4026540 | [ 3 ] 15404-2020972 |************************************************** [ 471 ] Storage Throughput = excellent ( 1039.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012700 bp ( 40012640 non ambiguous ) - Num Contigs Represented = 111 - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:21 (hh:mm:ss) Elapsed Time Round Time: 00:38:25 (hh:mm:ss) Elapsed Time : 299 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5519 repeats masked totaling 2218393 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025580 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10025580 bp After Masking: 6434103 bp Masked: 35.82 % -- Input Database Coverage: 10025580 bp out of 428417373 bp ( 2.34 % ) Sampling Time: 00:01:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:05:02 (hh:mm:ss) Elapsed Time, 8780 HSPs Collected Number of families returned by RECON: 845 Round Time: 00:07:41 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17919 repeats masked totaling 7330459 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027287 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 30027227 bp After Masking: 18214062 bp Masked: 39.34 % -- Input Database Coverage: 40052867 bp out of 428417373 bp ( 9.35 % ) Sampling Time: 00:04:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:25:14 (hh:mm:ss) Elapsed Time, 46761 HSPs Collected Number of families returned by RECON: 3202 Round Time: 00:31:08 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56131 repeats masked totaling 20791629 bp(s). - TE Masking time 00:02:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032095 bp Num Contigs Represented = 158 Non ambiguous bp: Initial: 90032075 bp After Masking: 57027994 bp Masked: 36.66 % -- Input Database Coverage: 130084962 bp out of 428417373 bp ( 30.36 % ) Sampling Time: 00:13:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2609470 Comparison Time: 03:02:40 (hh:mm:ss) Elapsed Time, 177950 HSPs Collected Number of families returned by RECON: 14075 Round Time: 03:24:59 (hh:mm:ss) Elapsed Time : 267 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 205990 repeats masked totaling 72497781 bp(s). - TE Masking time 00:08:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270037367 bp Num Contigs Represented = 368 Non ambiguous bp: Initial: 270037247 bp After Masking: 159961730 bp Masked: 40.76 % -- Input Database Coverage: 400122329 bp out of 428417373 bp ( 93.40 % ) Sampling Time: 00:44:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23615628 Comparison Time: 22:33:57 (hh:mm:ss) Elapsed Time, 1013066 HSPs Collected Number of families returned by RECON: 51940 Round Time: 24:32:18 (hh:mm:ss) Elapsed Time : 695 families discovered. RepeatScout/RECON discovery complete: 1313 families found Classification Time: 01:16:17 (hh:mm:ss) Elapsed Time Program Time: 30:30:48 (hh:mm:ss) Elapsed Time