RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.qjvtkC/RM_27599.ThuJul42304342024 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: 1720159473 Database = /dev/shm/rModeler.qjvtkC/GCF_000690725.1_Stegastes_partitus-1.0.2 - Sequences = 5817 - Bases = 800485922 - N50 = 413264 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 3122250-3345205 | [ 1 ] 2899296-3122250 | [ ] 2676342-2899296 | [ ] 2453388-2676342 | [ 1 ] 2230434-2453388 | [ 2 ] 2007479-2230433 | [ 6 ] 1784525-2007479 | [ 5 ] 1561571-1784525 | [ 6 ] 1338617-1561571 | [ 9 ] 1115663-1338617 | [ 28 ] 892708-1115662 | [ 46 ] 669754-892708 |* [ 105 ] 446800-669754 |*** [ 281 ] 223846-446800 |******** [ 789 ] 892-223846 |************************************************** [ 4538 ] Storage Throughput = excellent ( 1047.22 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42843455 bp ( 40037492 non ambiguous ) - Num Contigs Represented = 994 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:22 (hh:mm:ss) Elapsed Time Round Time: 00:23:15 (hh:mm:ss) Elapsed Time : 420 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8424 repeats masked totaling 1070857 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10717669 bp Num Contigs Represented = 296 Non ambiguous bp: Initial: 10016423 bp After Masking: 8866769 bp Masked: 11.48 % -- Input Database Coverage: 10717669 bp out of 800485922 bp ( 1.34 % ) Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 48205 Comparison Time: 00:06:31 (hh:mm:ss) Elapsed Time, 10980 HSPs Collected Number of families returned by RECON: 1752 Round Time: 00:07:23 (hh:mm:ss) Elapsed Time : 35 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29148 repeats masked totaling 3858200 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32125756 bp Num Contigs Represented = 791 Non ambiguous bp: Initial: 30021039 bp After Masking: 25946906 bp Masked: 13.57 % -- Input Database Coverage: 42843425 bp out of 800485922 bp ( 5.35 % ) Sampling Time: 00:01:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 472878 Comparison Time: 00:43:04 (hh:mm:ss) Elapsed Time, 62465 HSPs Collected Number of families returned by RECON: 5710 Round Time: 00:46:34 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 103185 repeats masked totaling 15508160 bp(s). - TE Masking time 00:01:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 95732341 bp Num Contigs Represented = 1795 Non ambiguous bp: Initial: 90010282 bp After Masking: 73816969 bp Masked: 17.99 % -- Input Database Coverage: 138575766 bp out of 800485922 bp ( 17.31 % ) Sampling Time: 00:04:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 4171716 Comparison Time: 04:33:17 (hh:mm:ss) Elapsed Time, 225419 HSPs Collected Number of families returned by RECON: 18911 Round Time: 04:52:36 (hh:mm:ss) Elapsed Time : 389 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 378602 repeats masked totaling 58556502 bp(s). - TE Masking time 00:08:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 288423806 bp Num Contigs Represented = 3448 Non ambiguous bp: Initial: 270034331 bp After Masking: 209407745 bp Masked: 22.45 % -- Input Database Coverage: 426999572 bp out of 800485922 bp ( 53.34 % ) Sampling Time: 00:17:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 37788471 Comparison Time: 35:56:53 (hh:mm:ss) Elapsed Time, 690350 HSPs Collected Number of families returned by RECON: 74573 Round Time: 38:30:21 (hh:mm:ss) Elapsed Time : 1040 families discovered. RepeatScout/RECON discovery complete: 2027 families found Classification Time: 01:10:19 (hh:mm:ss) Elapsed Time Program Time: 45:50:28 (hh:mm:ss) Elapsed Time