RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.lAvroD/RM_18122.TueJan160325412024 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: 1705404340 Database = /dev/shm/rModeler.lAvroD/GCA_963457635.1_fMicVar1.1 - Sequences = 188 - Bases = 724694306 - N50 = 30221424 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 44376632-47546321 | [ 2 ] 41206944-44376632 | [ ] 38037256-41206944 | [ 2 ] 34867568-38037256 | [ 1 ] 31697880-34867568 | [ 3 ] 28528192-31697880 |* [ 4 ] 25358504-28528192 |* [ 5 ] 22188816-25358504 | [ 2 ] 19019128-22188816 |* [ 4 ] 15849440-19019128 | [ ] 12679752-15849440 | [ ] 9510064-12679752 | [ ] 6340376-9510064 | [ ] 3170688-6340376 | [ ] 1000-3170688 |************************************************** [ 165 ] Storage Throughput = excellent ( 1057.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012593 bp ( 40008593 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:38 (hh:mm:ss) Elapsed Time Round Time: 00:31:41 (hh:mm:ss) Elapsed Time : 589 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 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11287 repeats masked totaling 1704559 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021856 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10021056 bp After Masking: 7182850 bp Masked: 28.32 % -- Input Database Coverage: 10021856 bp out of 724694306 bp ( 1.38 % ) Sampling Time: 00:01:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:55 (hh:mm:ss) Elapsed Time, 8768 HSPs Collected Number of families returned by RECON: 1577 Round Time: 00:07:42 (hh:mm:ss) Elapsed Time : 18 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 00:04:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34541 repeats masked totaling 5398956 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030657 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30027457 bp After Masking: 20996621 bp Masked: 30.08 % -- Input Database Coverage: 40052513 bp out of 724694306 bp ( 5.53 % ) Sampling Time: 00:06:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:32:53 (hh:mm:ss) Elapsed Time, 82005 HSPs Collected Number of families returned by RECON: 5628 Round Time: 00:41:26 (hh:mm:ss) Elapsed Time : 126 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 115401 repeats masked totaling 18320723 bp(s). - TE Masking time 00:01:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012899 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 90001899 bp After Masking: 59808874 bp Masked: 33.55 % -- Input Database Coverage: 130065412 bp out of 724694306 bp ( 17.95 % ) Sampling Time: 00:23:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 04:13:26 (hh:mm:ss) Elapsed Time, 286215 HSPs Collected Number of families returned by RECON: 18145 Round Time: 04:53:24 (hh:mm:ss) Elapsed Time : 432 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:09:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 405429 repeats masked totaling 65651907 bp(s). - TE Masking time 00:10:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270071144 bp Num Contigs Represented = 127 Non ambiguous bp: Initial: 270036660 bp After Masking: 169412721 bp Masked: 37.26 % -- Input Database Coverage: 400136556 bp out of 724694306 bp ( 55.21 % ) Sampling Time: 01:25:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 28:16:37 (hh:mm:ss) Elapsed Time, 910547 HSPs Collected Number of families returned by RECON: 67245 Round Time: 31:53:01 (hh:mm:ss) Elapsed Time : 1107 families discovered. RepeatScout/RECON discovery complete: 2272 families found Classification Time: 01:27:06 (hh:mm:ss) Elapsed Time Program Time: 39:34:20 (hh:mm:ss) Elapsed Time