RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.srcKMQ/RM_866.TueJan160257112024 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: 1705402630 Database = /dev/shm/rModeler.srcKMQ/GCA_963457725.1_fSprSpr1.1 - Sequences = 387 - Bases = 840332306 - N50 = 37234460 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 73655078-78916084 | [ 1 ] 68394072-73655077 | [ 1 ] 63133067-68394072 | [ ] 57872061-63133066 | [ 1 ] 52611056-57872061 | [ ] 47350050-52611055 | [ 1 ] 42089044-47350049 | [ 1 ] 36828039-42089044 | [ 2 ] 31567033-36828038 |* [ 11 ] 26306028-31567033 | [ 2 ] 21045022-26306027 | [ ] 15784016-21045021 | [ 1 ] 10523011-15784016 | [ ] 5262005-10523010 | [ ] 1000-5262005 |************************************************** [ 366 ] Storage Throughput = excellent ( 1033.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40049179 bp ( 40037753 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:29:55 (hh:mm:ss) Elapsed Time Round Time: 00:45:26 (hh:mm:ss) Elapsed Time : 598 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6672 repeats masked totaling 1561229 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003510 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10000310 bp After Masking: 7090722 bp Masked: 29.09 % -- Input Database Coverage: 10003510 bp out of 840332306 bp ( 1.19 % ) Sampling Time: 00:03:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:07:07 (hh:mm:ss) Elapsed Time, 5960 HSPs Collected Number of families returned by RECON: 1325 Round Time: 00:10:35 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19844 repeats masked totaling 4669991 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30045665 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30037439 bp After Masking: 21747563 bp Masked: 27.60 % -- Input Database Coverage: 40049175 bp out of 840332306 bp ( 4.77 % ) Sampling Time: 00:07:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:36:10 (hh:mm:ss) Elapsed Time, 47621 HSPs Collected Number of families returned by RECON: 4906 Round Time: 00:45:32 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66002 repeats masked totaling 14670817 bp(s). - TE Masking time 00:03:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041908 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 90007556 bp After Masking: 64565408 bp Masked: 28.27 % -- Input Database Coverage: 130091083 bp out of 840332306 bp ( 15.48 % ) Sampling Time: 00:24:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 04:37:21 (hh:mm:ss) Elapsed Time, 334715 HSPs Collected Number of families returned by RECON: 16240 Round Time: 05:19:55 (hh:mm:ss) Elapsed Time : 500 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:53:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 256180 repeats masked totaling 59973402 bp(s). - TE Masking time 00:17:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270121273 bp Num Contigs Represented = 184 Non ambiguous bp: Initial: 270027093 bp After Masking: 179250018 bp Masked: 33.62 % -- Input Database Coverage: 400212356 bp out of 840332306 bp ( 47.63 % ) Sampling Time: 01:18:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23293725 Comparison Time: 30:40:46 (hh:mm:ss) Elapsed Time, 1096153 HSPs Collected Number of families returned by RECON: 58018 Round Time: 34:04:08 (hh:mm:ss) Elapsed Time : 1279 families discovered. RepeatScout/RECON discovery complete: 2450 families found Classification Time: 02:37:57 (hh:mm:ss) Elapsed Time Program Time: 43:43:33 (hh:mm:ss) Elapsed Time