RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.UIbQL9/RM_12917.ThuDec72341142023 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: 1702021272 Database = /dev/shm/rModeler.UIbQL9/GCA_949987615.1_fPolPol2.1 - Sequences = 616 - Bases = 606767444 - N50 = 27710796 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 49900425-53464670 | [ 3 ] 46336180-49900424 | [ ] 42771936-46336180 | [ ] 39207691-42771935 | [ ] 35643446-39207690 | [ ] 32079202-35643446 | [ 1 ] 28514957-32079201 | [ 1 ] 24950712-28514956 | [ 4 ] 21386468-24950712 | [ 8 ] 17822223-21386467 | [ 3 ] 14257978-17822222 | [ ] 10693734-14257978 | [ ] 7129489-10693733 | [ ] 3565244-7129488 | [ ] 1000-3565244 |************************************************** [ 596 ] Storage Throughput = excellent ( 1102.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029385 bp ( 40008585 non ambiguous ) - Num Contigs Represented = 83 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:45 (hh:mm:ss) Elapsed Time Round Time: 00:28:53 (hh:mm:ss) Elapsed Time : 403 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 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4599 repeats masked totaling 842622 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029001 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10022801 bp After Masking: 7596104 bp Masked: 24.21 % -- Input Database Coverage: 10029001 bp out of 606767444 bp ( 1.65 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:05:48 (hh:mm:ss) Elapsed Time, 4476 HSPs Collected Number of families returned by RECON: 1015 Round Time: 00:08:10 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17178 repeats masked totaling 3483077 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040375 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 30025775 bp After Masking: 22743504 bp Masked: 24.25 % -- Input Database Coverage: 40069376 bp out of 606767444 bp ( 6.60 % ) Sampling Time: 00:05:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 294528 Comparison Time: 00:32:01 (hh:mm:ss) Elapsed Time, 46991 HSPs Collected Number of families returned by RECON: 4302 Round Time: 00:39:53 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56924 repeats masked totaling 10787758 bp(s). - TE Masking time 00:02:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90088120 bp Num Contigs Represented = 136 Non ambiguous bp: Initial: 90037258 bp After Masking: 67847816 bp Masked: 24.64 % -- Input Database Coverage: 130157496 bp out of 606767444 bp ( 21.45 % ) Sampling Time: 00:17:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2648451 Comparison Time: 03:55:08 (hh:mm:ss) Elapsed Time, 255433 HSPs Collected Number of families returned by RECON: 15917 Round Time: 04:27:14 (hh:mm:ss) Elapsed Time : 399 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 224892 repeats masked totaling 46554040 bp(s). - TE Masking time 00:12:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270184183 bp Num Contigs Represented = 349 Non ambiguous bp: Initial: 270021653 bp After Masking: 189262313 bp Masked: 29.91 % -- Input Database Coverage: 400341679 bp out of 606767444 bp ( 65.98 % ) Sampling Time: 00:59:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23877505 Comparison Time: 29:15:30 (hh:mm:ss) Elapsed Time, 906577 HSPs Collected Number of families returned by RECON: 55844 Round Time: 32:01:28 (hh:mm:ss) Elapsed Time : 1012 families discovered. RepeatScout/RECON discovery complete: 1887 families found Classification Time: 01:51:10 (hh:mm:ss) Elapsed Time Program Time: 39:36:48 (hh:mm:ss) Elapsed Time