RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GAPuq7/RM_16003.FriJul121701392024 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: 1720828898 Database = /dev/shm/rModeler.GAPuq7/GCF_002872115.1_PKINGS_0.1 - Sequences = 4666 - Bases = 799417351 - N50 = 1736529 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 6773385-7257134 | [ 3 ] 6289637-6773385 | [ 1 ] 5805889-6289637 | [ 3 ] 5322140-5805888 | [ 2 ] 4838392-5322140 | [ 3 ] 4354644-4838392 | [ 8 ] 3870895-4354643 | [ 3 ] 3387147-3870895 | [ 13 ] 2903399-3387147 | [ 17 ] 2419650-2903398 | [ 22 ] 1935902-2419650 | [ 37 ] 1452154-1935902 | [ 52 ] 968405-1452153 |* [ 90 ] 484657-968405 |* [ 147 ] 909-484657 |************************************************** [ 4265 ] Storage Throughput = excellent ( 1180.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43402340 bp ( 40025746 non ambiguous ) - Num Contigs Represented = 702 - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:01 (hh:mm:ss) Elapsed Time Round Time: 00:21:25 (hh:mm:ss) Elapsed Time : 495 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 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8498 repeats masked totaling 1256343 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10826323 bp Num Contigs Represented = 240 Non ambiguous bp: Initial: 10037289 bp After Masking: 8571606 bp Masked: 14.60 % -- Input Database Coverage: 10826323 bp out of 799417351 bp ( 1.35 % ) Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 48828 Comparison Time: 00:06:50 (hh:mm:ss) Elapsed Time, 6328 HSPs Collected Number of families returned by RECON: 1362 Round Time: 00:07:43 (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 : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25436 repeats masked totaling 3853862 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32616417 bp Num Contigs Represented = 592 Non ambiguous bp: Initial: 30023901 bp After Masking: 25559392 bp Masked: 14.87 % -- Input Database Coverage: 43442740 bp out of 799417351 bp ( 5.43 % ) Sampling Time: 00:01:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 477753 Comparison Time: 00:36:42 (hh:mm:ss) Elapsed Time, 45362 HSPs Collected Number of families returned by RECON: 4823 Round Time: 00:39:47 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86909 repeats masked totaling 13706692 bp(s). - TE Masking time 00:01:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 98113831 bp Num Contigs Represented = 1130 Non ambiguous bp: Initial: 90006922 bp After Masking: 74373019 bp Masked: 17.37 % -- Input Database Coverage: 141556571 bp out of 799417351 bp ( 17.71 % ) Sampling Time: 00:04:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 4142881 Comparison Time: 04:07:13 (hh:mm:ss) Elapsed Time, 252433 HSPs Collected Number of families returned by RECON: 15570 Round Time: 04:24:35 (hh:mm:ss) Elapsed Time : 516 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 325026 repeats masked totaling 53640968 bp(s). - TE Masking time 00:08:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 292947002 bp Num Contigs Represented = 2269 Non ambiguous bp: Initial: 270033741 bp After Masking: 210940841 bp Masked: 21.88 % -- Input Database Coverage: 434503573 bp out of 799417351 bp ( 54.35 % ) Sampling Time: 00:18:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 37078966 Comparison Time: 30:48:22 (hh:mm:ss) Elapsed Time, 690555 HSPs Collected Number of families returned by RECON: 54242 Round Time: 32:36:52 (hh:mm:ss) Elapsed Time : 1116 families discovered. RepeatScout/RECON discovery complete: 2247 families found Classification Time: 01:27:32 (hh:mm:ss) Elapsed Time Program Time: 39:37:54 (hh:mm:ss) Elapsed Time