RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Lrm44l/RM_2851947.TueApr151120572025 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: 1744741255 Database = /dev/shm/rModeler.Lrm44l/GCA_042242135.1_fArrGeo1.hap2 - Sequences = 552 - Bases = 801586327 - N50 = 28692490 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 33627466-36028805 | [ 1 ] 31226128-33627466 | [ 5 ] 28824790-31226128 | [ 5 ] 26423452-28824790 | [ 4 ] 24022114-26423452 | [ 5 ] 21620776-24022114 | [ 1 ] 19219438-21620776 | [ 2 ] 16818099-19219437 | [ ] 14416761-16818099 | [ ] 12015423-14416761 | [ 1 ] 9614085-12015423 | [ ] 7212747-9614085 | [ ] 4811409-7212747 | [ ] 2410071-4811409 | [ ] 8733-2410071 |************************************************** [ 528 ] Storage Throughput = excellent ( 1712.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010032 bp ( 40009632 non ambiguous ) - Num Contigs Represented = 155 - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:53 (hh:mm:ss) Elapsed Time Round Time: 00:19:14 (hh:mm:ss) Elapsed Time : 275 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5857 repeats masked totaling 1396588 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030175 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 10029975 bp After Masking: 7926699 bp Masked: 20.97 % -- Input Database Coverage: 10030175 bp out of 801586327 bp ( 1.25 % ) Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:47 (hh:mm:ss) Elapsed Time, 43533 HSPs Collected Number of families returned by RECON: 1423 Round Time: 00:03:51 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19861 repeats masked totaling 5675811 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019777 bp Num Contigs Represented = 133 Non ambiguous bp: Initial: 30019577 bp After Masking: 22211743 bp Masked: 26.01 % -- Input Database Coverage: 40049952 bp out of 801586327 bp ( 5.00 % ) Sampling Time: 00:01:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:12:10 (hh:mm:ss) Elapsed Time, 59555 HSPs Collected Number of families returned by RECON: 5249 Round Time: 00:14:32 (hh:mm:ss) Elapsed Time : 114 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 74173 repeats masked totaling 20270770 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028381 bp Num Contigs Represented = 263 Non ambiguous bp: Initial: 90027381 bp After Masking: 64347540 bp Masked: 28.52 % -- Input Database Coverage: 130078333 bp out of 801586327 bp ( 16.23 % ) Sampling Time: 00:04:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2604903 Comparison Time: 01:15:33 (hh:mm:ss) Elapsed Time, 270974 HSPs Collected Number of families returned by RECON: 18729 Round Time: 01:24:58 (hh:mm:ss) Elapsed Time : 407 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 279953 repeats masked totaling 72364725 bp(s). - TE Masking time 00:02:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032867 bp Num Contigs Represented = 428 Non ambiguous bp: Initial: 270026267 bp After Masking: 181533464 bp Masked: 32.77 % -- Input Database Coverage: 400111200 bp out of 801586327 bp ( 49.91 % ) Sampling Time: 00:15:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23423590 Comparison Time: 08:47:43 (hh:mm:ss) Elapsed Time, 1577342 HSPs Collected Number of families returned by RECON: 67281 Round Time: 09:41:24 (hh:mm:ss) Elapsed Time : 1083 families discovered. RepeatScout/RECON discovery complete: 1895 families found Classification Time: 00:36:21 (hh:mm:ss) Elapsed Time Program Time: 12:20:20 (hh:mm:ss) Elapsed Time